The major difference was that apartheid was the *national* policy of the South African government, and it was codified into law in a way that American segregation wasn’t. This doesn’t mean that Jim Crow laws didn’t exist, they did, but those were state laws, not federal. A black man living in the South had the same constitutional rights as a white man, at least on paper. In South Africa, there was an entire racial hierarchy, with multiple levels, coded into the law. And this went well beyond separate bathrooms and schools. Non-whites had different IDs, had travel restrictions that whites didn’t and on and on.
tl;dr: The totality of apartheid went way beyond anything seen in the U.S.
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