In Durban, I recently ate a place called Spice on Florida that I liked a lot. This is in one of the nicer residential neighborhoods, well away from the touristy waterfront area (which I would stay well away from if you want to eat "good" food).

In Cape Town, there are plenty of places on the waterfront (One.Waterfront gets great reviews although I have not been there--it is very expensive; Five Flies is another well-regarded place). If you are not going to be hitting wine country at all, and if you have access to a car, I'd recommend a place called Constantia Uitsig, which is fine dining in a winery located very close to Cape Town in the suburb of Constantia. Go for lunch--it's a beautiful setting and really nice food.

South Africa has a lot of great restaurants but it also has a lot of "theme" restaurants/chains that focus more on the decor than the food. I find Moyo to be in this category--there are branches in several cities. Another thing you may find is that eating well sometimes means eating in a shopping mall, odd as that sounds. The safety concerns (sometimes safety of your car, sometimes safety of your person) in some SA cities, particularly Jo'burg and Durban, have pushed a lot of restaurants into malls and gated office parks. It's slightly weird but the food can still be good.