ASSAf Science-for-Society Gold Medals are the apex awards of the Academy and the South African science system and are awarded in recognition of outstanding achievements by individuals. Up to two gold medals are awarded per annum for outstanding achievement in scientific thinking for the benefit of society. The first Gold Medals were awarded in 2003. 

The AU-TWAS award scheme aims to recognise and reward talented young scientists in Africa. The AU-TWAS Prize for Young Scientists in South Africa is managed by ASSAf, on behalf of its partners, the African Union Commission (AUC), The World Academy of Sciences (TWAS) and the Department of Science and Technology (DST).

The ASSAf Humanities Book Award is presented to a writer/s of a scholarly, well-written work of non-fiction, published up to three years prior to its nomination. The book should be noteworthy in its contribution to developing new understanding and insight of a topic in the Humanities.

In 2008, ASSAf introduced the prestigious Gold Medal for Outstanding Meritorious Service to recognise exceptional service to the Academy. The award is not offered on a regular basis each year and has only been awarded twice since its inception.

The award was established when Dr Sydney Brenner donated a portion of his 2002 Nobel Prize to ASSAf to permit ASSAf (in partnership with the Oppenheimer Memorial Trust) to offer a prestigious postdoctoral Fellowship for research in molecular biology to be undertaken in South Africa over two years by an outstanding young scientist.