Country of My Skull is a 1998 nonfiction book by Antjie Krog primarily about the findings of the South African Truth and Reconciliation Commission, as per Google, and it was the foundation text of my History of South Africa course at Wellesley.

Saul Dubow's 2014 history of apartheid from Oxford, David Welsh's Rise and Fall of Apartheid (2011), and other specific works like Desmond Tutu (No Future Without Forgiveness) are worthwhile. In the first two, you have good bibliographies. Some key exposes like The Cordoned Heart and Ernest Cole's House of Bondage--the latter hard to get but absolutely gutwrenching in its photography, by a black photographer who escaped SA--are also very moving for students. I can't write more at present because I am actually in the field in South Africa--but I may have more specific notes if necessary.

I'm pretty sure /u/khosikulu can recommend a great many histories.

I'd like to plug more of a first-person/new journalism account, Rian Malan's My Traitor's Heart, which is a really good read that comes at things from a more emotional perspective while still encompassing the facts of apartheid, from its inception (his ancestor was one of the architects of the ideology) to the despair the system engendered in what turned out to be its final years.

Here's the NY Times review when it came out.

I'm also a fan of H.C. Bosman, but that's even more on the cultural side - he was a journalist who wrote some sardonic, clever, well-crafted short stories in the 1930s and 40s. Very good at capturing Boer culture and attitudes, though not a great source of facts. Mafeking Road is probably the best collection to start with.