The other two teams in the group are Ethiopia and Madagascar.
Nigeria and Guinea were last drawn together in the qualifying series for the FIFA 1998 World Cup.
A total of forty four teams were drawn into 11 groups. The group winners and three of the best second placed teams will qualify for the 28th African Nations Cup.
World Cup 2010 hosts South Africa have been handed a testing draw in Group 7 with defending champions Egypt, Sierra Leone and Niger.
Equatorial Guinea and Gabon qualify automatically as co-hosts.
The Full draw: Group 1 Mali, Cape Verde, Zimbabwe, Liberia
Group 2 Nigeria, Guinea, Ethiopia, Madagascar
Group 3 Zambia, Mozambique, Libya, Comores
Group 4 Algeria, Morocco, Tanzania, Central African Republic
Group 5 Cameroon, Senegal, DR Congo, Mauritius
Group 6 Burkina Faso, Gambia, Namibia, Mauritania
Group 7 Egypt, South Africa, Sierra Leone, Niger
Group 8 Ivory Coast, Benin, Rwanda, Burundi
Group 9 Ghana, Congo, Sudan, Swaziland
Group 10 Angola, Uganda, Kenya, Guinea-Bissau
Group 11 Tunisia, Malawi, Chad, Botswana