A health ministry statement declared "a total travel ban for all non-citizens travelling from these high risk countries," referring to Guinea, Liberia and Sierra Leone.
South Africans returning home from these areas will undergo strict screening, it added.
Authorities also barred non-essential travel to the three countries.
South Africa has so far been Ebola-free despite two scares in as many weeks: a South African man returning from Liberia and a Guinean woman.
Both tested negative.
Johannesburg is a major hub for air travel between southern Africa and the rest of the continent.
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