The answer to this can be found in Chapter 19. Specifically, it can be found on pages 396 and 397 in the hardcover edition of the book.
In Chapter 19, Diamond is arguing that the Bantu were able to dominate Africa because they had agriculture while other races of people in Southern Africa did not. This is how “Africa became black.” Diamond has argued throughout the book that people with agriculture will dominate those who do not have it.
However, he says, the Khoisan were not completely dominated by the Bantu. The reason for this has to do with geography. Diamond says that, once you go south of the Fish River in what is now South Africa, the rain patterns are no longer good for the crops that the Bantu grew. The Bantu grew crops that needed rain in the summer. In this area of South Africa, rains fell mainly in the winter. This meant that the Bantu’s crops could not thrive in this area. This made them unable to dominate that area and, as a result, the Khoisan were able to survive.