How have African countries kept the boundaries divided by colonists and countries unified for decades, despite the many ethnical groups and conflicts?

The reasons why African countries have, in most cases, maintained the borders they inherited from the colonial powers are summarized below. Note that, given how broad the question is, some factors may apply to some countries but not to others.

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1. Both the Organization of African Unity (OAU) and most leaders of individual states have specifically rejected any alterations. Although this has been largely observed by member states, borders in the Horn of Africa have been disputed.

The OAU, founded in 1963, wasted little time in making this known:

the OAU has been basically interested in preventing conflicts among African states, and this tendency is traceable in the 1964 Cairo Resolution, where it was affirmed that: “All Member States pledge themselves to respect the borders existing on their achievement of national independence”

Source: Marco Zoppi, 'The OAU and the Question of Borders'. In Journal of African Union Studies (2013)

This stance was affirmed by individual heads of state even before the formation of the OAU. For example, Abubakar Tafawa Balewa, the first prime Minister of Nigeria stated before the UN in 1960:

"The colonizing powers of the last century partitioned Africa in haphazard and artificial manner and drew boundaries which cut right across former groupings. Yet, however artificial those boundaries were at first the countries they have created have come to regard themselves as units independent of one another. We have seen them all seeking admission to this Organizations as separate states. It is, therefore, our policy to leave those boundaries as they are at present, and to discourage any adjustment whatsoever...."

Cited in: Zoppi

Also, Philippe Tsiranana, President of Madagascar, said in 1963:

"It is no longer possible neither desirable to change the borders of nations in the name of racial or religious grounds; indeed, if we take race, tribe or religion as parameter for our boundaries, there would be in Africa States that would be erased from the map” (author's translation)

Cited in: Zoppi

The key reason underlining this commitment to existing borders has always been that encouraging or supporting separatist movements in other countries could easily backfire, i.e. other states could retaliate by instigating secessionist movements, creating a domino effect which would benefit none of the ruling elites. Further, supporting a secessionist movement in another country could encourage rebellions in one's own country (as happened in the Cote d'Ivoire with the Anyi / Agni - see below).

The conflicts that have erupted over borders have, with some exceptions, mostly been over resources (see, for example, the Agacher Strip War between Burkina Faso and Mali, and Rukwanzi Island dispute between the Congo and Uganda) rather than ethnicity, and have occurred in areas where the borders were poorly demarcated by the colonial powers.

The most notable exception to the general acceptance of colonial borders has been in the Horn of Africa. Somalia and Ethiopia fought over the

Ogaden region in 1977-78. A conflict between Ethiopia and Kenya is recorded in 1963; while Somalia and Kenya will fight over borders until 1984, when an agreement is finally reached. Moreover, the Region is devastated by the Eritrean independence in 1993 and the subsequent Eritrean-Ethiopian War which took place between 1998 and 2000.

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2. Most states have unitary forms of government rather than federal, making it more difficult for regional power-bases to develop.

In Francophone Africa, unitary forms of government were mostly inherited and kept in place, though Cameroon tried and then dropped the federal system. Former British colonies were

often bequeathed federal or quasi-federal institutions to its ex-colonies. Nigeria, Kenya, Ghana, the Federation of Rhodesia and Nyasaland and Uganda's amorphous and contradictory federal-unitary relations between sub-national units and the centre are examples.

Source: J. Isawa ELAIGWU, 'Nation-building and changing political structure.' In 'General History of Africa, vol. 8' (1993)

However, of the above, only Nigeria is still federal. Ghana under President Kwame Nkrumah was the first to abandon federalism in favour of a unitary system. Unitary systems of government made it easier for the new states to promote national unity as a

unitary system is more likely to engender harmony among the various ethnic groups in the country leading to internal stability.

Note that this is in marked contrast to the former Yugoslavia where the federal republics exercised considerable power, especially after 1974, which facilitated the later break-up. That Nigeria has not broken up as Yugoslavia did can probably be mostly attributed to the lessons learnt in the wake of the Biafran conflict. In Nigeria, although there are marked ethnic tensions between politicians,

the army has adopted a discourse that is marked by nationalism and unity....the Nigerian army has clearly taken on the role as a national integrator.

Source: Florence Gaub, 'Military Integration After Civil Wars: Multiethnic Armies, Identity and Post-Conflict Reconstruction' (2010)

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3. Those unitary states which didn't start out as one-party states soon drifted away from a democratic multi-party system, further strengthening the control of the heads of states who wielded power not only through the party they controlled but also through expanding bureaucracies.

As observed by J. Isawa Elaigwu,

In many states, the trend has been in the direction of one-party state or one-party-dominant state - for example, KANU in Kenya, the C P P in Ghana, the Union démocratique voltaïque in Upper Volta (now Burkina Faso), the Union soudanaise in Mali, the Parti démocratique de la Côte d'Ivoire (PDCI) in Côte d'Ivoire (as from 1957), and the Malawi Congress Party (as from 1966). In Senegal, the Union progressiste sénégalaise (UPS) has been the dominant party in the state. In Cameroon, the Union nationale camerounaise became the only party as from 1966.

These single parties invariably encompassed all ethnic groups, including the elites in whose interests it has been to promote the state, the prime dispenser of patronage. They also promoted nationalism, sometimes so successfully that it has led to anti-foreigner riots (on which more below). Further,

...the central bureaucracy in post-colonial African societies expanded rapidly....This was mainly because bureaucracies were seen as institutions for political control.

Source: J. Isawa Elaigwu

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4. Most separatist movements' armed strength has proven no match for the armed forces of the states they were in conflict with, even though many of these armed forces have often been poorly-equipped and trained.

This has proven to be the case even when the separatist movement did manage to obtain some outside support, a notable example being Biafra which received substantial support from a French government looking to undermine (Anglophone) Nigeria. French pressure led to a number of its former colonies also supporting Biafra. Ironically, among these were Cote d'Ivoire where the Anyi (Agni) ethnic group had sought separation in 1960 on the eve of Ivorian independence; encouraged by the Biafran example, they again revolted in 1969 but were easily crushed by the Ivorian army.

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5. The former colonial powers, especially France, have almost always strongly opposed any changes in borders. Consequently, separatist movements have usually been denied meaningful international military, financial and diplomatic support.

The Biafrans, as noted above, did manage to obtain the support of France and a few others but with Britain (the former colonial power), the Soviet Union and others backing Nigeria it was a lost cause. For the most part, though, it has been in France's political and economic interests to maintain both peace and existing borders:

Even after the dissolution of its empire in the 1950s and 1960s, France considered its former colonies to be a pr´e carr´e (private domain) or chasse gard´ee (private hunting ground) – off limits to other powers, much as the United States applied the Monroe Doctrine to Latin America...

By the late 1970s, some 15,000 French troops were still garrisoned in more than twenty African states and territories...As late as 1993, a rapid deployment force of 44,500 men was ready to leave France on short notice to protect French interests in Africa.

Source: Elizabeth Schmidt, ‘Foreign Intervention in Africa: From the Cold War to the War on Terror’ (2013)

These interests were primarily economic. In addition to consistently running a large trade surplus at the expense of its former colonies,

France was guaranteed access to strategic raw materials in the signatory countries. Most important among these were oil, natural gas, and uranium, the critical element in nuclear-power production.

In West Africa at least, it has been in France's interests to maintain peace and stability by preventing conflict both between and within states, though France has supported regime (not border) changes where it was in her interests to do so.

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6. The perception that ethnic groups had a strong sense of nationhood prior to colonization is, for the most part, greatly over-stated (Somalis being perhaps the most notable exception). Nor is there a contradiction in people seeing themselves as belonging to both an ethnic group and to a state.

For much of Africa, there were no clearly defined national boundaries before colonization took hold. Further, individuals saw themselves primarily as being part of a village community; their perception of nationhood bore little resemblance to the European perception. Thus, as observed in a study by William F. S. Miles and David A. Rochefort,

Hausa villagers on the Nigeria/Niger border “do not place their ethnic identity as Hausas above their national one as citizens of Nigeria or Niger and express greater affinity for non-Hausa cocitizens than foreign Hausas.”

Source: Jeffrey Herbst, ‘States and Power in Africa: Comparative Lessons in Authority and Control’ (2000)

The idea that there is necessarily a conflict between membership of an ethnic group and of the state is false. In the words of the Nigerian academic J. Isawa Elaigwu,

For us the process of nation-building does not involve the transfer of 'commitments and loyalties' from narrow or parochial levels of ethnic groups to a larger political unit such as Nigeria. That you are an Igbo, a Yoruba, or a Kikuyu, is a matter of identity. You cannot transfer it. You cannot cease being an Igbo or a Hausa or a Kikuyu simply because you so declare. For us it involves the widening (rather than transfer) of horizons of identity of parochial units to include larger units such as the state.

Further,

...contrary to conventional wisdom, African boundaries have fundamentally changed the nature of population movements across the continent. As a result, citizenship has acquired a salience that is often greater than the ties between ethnic groups separated by a border.

Source: Jeffrey Herbst

The importance and rights of citizenship have been so heavily promoted by some states that it has sometimes spilled over into an uglier side of nationalism, which has sometimes seen peoples of the same broad ethnic groups pitted against each other. For example, there were frequent anti-foreigner riots in Côte d'Ivoire (foreigners made up at least 30% of the population in the 1970s and 1980s, and maybe as much as 50%). At various times these have targeted, among others, Ghanaians, Burkinabes and Malians. The significance of this is that almost 50% of Ghanaians and over 40% of Ivorians are from the Akan group, while the Malinke make up significant portions of the populations of both Côte d'Ivoire and Mali and the Senufo are spread over all four of the above countries. Most of these riots have been over the perception that these foreigners were taking jobs away from Ivorians, but Ghanaians and Ivorians have also fought over football matches in more recent times.

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Final Note

None of the above is to say that there haven't been numerous incidents, small and large, of military actions throughout the continent. Many of these have involved military coups and some have been civil wars, but very few have been about secession or changing borders. Rather, the aims of the opposing forces have been to gain control of the whole country, not to split it up as this would only create smaller, weaker and less wealthy states.

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Other sources:

Lauren Honig, 'Immigrant Political Economies and Exclusionary Policy in Africa'. In 'Comparative Politics, Vol. 48, No. 4 (July 2016), pp. 517-537

Emmanuelle Lavallée and Julie Lochard, 'The empire strikes back: French‐African trade after independence'. In Review of International Economics (Feb 2019)

Wafula Okumu, 'Resources and border disputes in Eastern Africa'. In Journal of Eastern African Studies, Volume 4, 2010 - Issue 2

Wikipedia pages of the countries named in the answer

Local sources/connections, personal experiences, newspaper reports etc. in Ghana, Côte d'Ivoire, Burkina Faso, Mali and Togo from the early 1980s to the mid 1990s.