I take the IAD-DKR/ACC-JNB route fairly often... I have never had to get off the plane. It won't trigger any sort of yellow fever requirement in SA. If you had actually done a stopover and had an immigration stamp from those places, and gotten back on, then it would be a different story. Your ticket stub will also say IAD-JNB (no mention of the stop on it). Technical/intermediary stops are also quite frequent on many regional routes within Sub-Saharan Africa, so it's considered pretty normal.