Upvote:3
It depends on whether they notice it (you don't have to disclose anything like that on the form like you do for other countries) and probably on the rest of your application.
If they do notice it, it might lead to a refusal, not because there is any formal rule that bans people who overstayed elsewhere but because it goes to your credibility: You now say you will leave the Schengen area in three months time but the last time you implicitly did that (namely for your visit to South Africa), you actually stayed longer illegally.
So the consulate could legitimately rule that your βintent to leave the territory of the Members states before the expiry of the visa could not be ascertainedβ, which is one of the standard reasons to refuse a visa.