The draw, which was held in DR Congo's second-largest city Lubumbashi, placed the Pharaohs in Group 7.
Egypt last faced South Africa in a friendly in November 2006 in London, winning 1-0 through a goal from striker Emad Meteb.
Egypt, winners of the last three editions, are highly unlikely to face difficulties reaching the 2012 Nations Cup, which will take place in Equatorial Guinea and Gabon.
The winners and the best three second-placed teams will qualify for the finals in 2012, as well as the 2013 competition in Libya.
The groups:
1- Mali, Cape Verde, Zimbabwe, Liberia
2- Nigeria, Guinea, Ethiopia, Madagascar
3- Zambia, Mozambique, Libya, Comoros
4- Algeria, Morocco, Tanzania, Central Africa
5- Cameroon, Senegal, DR Congo, Mauritius
6- Burkina Faso, Gambia, Namibia, Mauritania
7- Egypt, South Africa, Sierra Leone, Niger
8- Ivory Coast, Benin, Rwanda, Burundi
9- Ghana, Congo, Sudan, Swaziland
10- Angola, Uganda, Kenya, Guinea-Bissau
11- Tunisia, Malawi, Chad, Botswana