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Well, the phrase supranational came only into broader usage in the context of the EU. Apparently first written English usage in 1871.
Usually, it connotes a voluntary pooling of power/competence by sovereign nations. This is in contrast to political entities that came into being (at least in part) due to military conquest or where parts were pressured into joining. Also, supra-national requires the members to be nations.
Now of course you can argue about what is a nation and what is not, and what is conquest and what liberation. Depending on your definitions of those terms you get a different answer to your question.
But I think you could make a case that the EU is the first such union, for example:
The United Nations and League of Nations, are usually referred to as international organisations not supranational unions because their powers are much more limited than the EU's, the United Nations are not named The Union of Nations after all. Its members are represented through their executive branches only, whereas the EU has been granted the competence to enact its own laws and has a parliament which is directly elected by the member nations' citizens (even if its powers are currently limited).
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Since the notion of nation-states is rather new, I would say that there are many candidates for this title from ancient times.
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The very idea that a state has to be "national" is quite recent. So this question has no sense. In the beginning on 19th century the Sultan of the Ottoman empire was told that in Europe there are states where everyone speaks the same language and has the same religion. He laughed.
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I think you can go back farther in the history. For example the Roman Republic created something like a supranational political union since it created a system constisting of foedus and socii, in which different cultures and cities got under the reign of Rome by bilateral contracts.
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I guess the definitions of all these terms are highly opinion based. Throughout history there always were loose federations of tribes (which arguably doesn't fit because they were not meant to last and/or were usually ruled by one of the tribes).
The Holy Roman Empire was probably the first thing that meets your criteria.
One thing that history shows us though is that such loose political unions never last, either because they split or because they become more and more centralized.
edit: After reading some comments and answers: My initial understanding was that in order to be "supernational" it needs to be decentralized, which doesn't seem to be the case.