So far as I can tell, there is no plural form, although perhaps other Rad Ref librarians will come up with an example. I just checked the Oxford English Dictionary online (it requires a subscription, but your local library may have one), which says
Name given in South Africa to the segregation of the inhabitants of European descent from the non-European (Coloured or mixed, Bantu, Indian, etc.); applied also to any similar movement elsewhere; also, to other forms of racial separation (social, educational, etc.). Also fig. and attrib.
I would say that "apartheid policies" would be your best bet for a plural form, though it might be worth explaining to your audience that the term can apply to many different segregation policies, not just the South African one that we usually associate with the word.
To soon to have a rule
Since apartheid was the name of a specific policy in a specific place, there would be no "official" plural, especially since the English language is governed by usage rather than a centralized authority, and apartheid is a relatively recent term. It has come to refer to extreme forms of segregation, where it becomes similar to other terms that describe political philosophies or practices - analogous to fascism, or democracy. So, it would not be incorrect to say apartheids the way one would say democracies, though it seems more clear to pattern similar to fascism, and say "apartheid governments," or as suggested above "apartheid policies."