| Saturday 8th September 2012 | |||
| 1st Leg | |||
| Cape Verde Islands | 2-0 | Cameroon | |
| Central African Rep | 1-0 | Burkina Faso | |
| Gabon | 1-1 | Togo | |
| Ghana | 2-0 | Malawi | |
| Ivory Coast | 4-2 | Senegal | |
| Liberia | 2-2 | Nigeria | |
| Mali | 3-0 | Botswana | |
| Sierra Leone | 2-2 | Tunisia | |
| Sudan | 5-3 | Ethiopia | |
| Zambia | 1-0 | Uganda | |
| Sunday 9th September 2012 | |||
| 1st Leg | |||
| Congo DR | 4-0 | Equatorial Guinea | |
| Guinea | 1-0 | Niger | |
| Libya | 0-1 | Algeria | (n) |
| Mozambique | 2-0 | Morocco | |
| Zimbabwe | 3-1 | Angola | |
| Saturday 13th October 2012 | |||
| 2nd Leg | |||
| Botswana | 1-4 | Mali | (1-7) |
| Malawi | 0-1 | Ghana | (0-3) |
| Morocco | 4-0 | Mozambique | (4-2) |
| Nigeria | 6-1 | Liberia | (8-3) |
| Senegal | 0-2 | Ivory Coast | (2-6) |
| (Ivory Coast awarded match) | |||
| Tunisia | 0-0 | Sierra Leone | (2-2) |
| (Tunisia won on away goals) | |||
| Uganda | 1-0 | Zambia | (1-1) |
| (Zambia won on penalties) | |||
| Sunday 14th October 2012 | |||
| 2nd Leg | |||
| Algeria | 2-0 | Libya | (3-0) |
| Angola | 2-0 | Zimbabwe | (3-3) |
| (Angola won on away goals) | |||
| Burkina Faso | 3-1 | Central African Rep | (3-2) |
| Cameroon | 2-1 | Cape Verde Islands | (2-3) |
| Equatorial Guinea | 2-1 | Congo DR | (2-5) |
| Ethiopia | 2-0 | Sudan | (5-5) |
| (Ethiopia won on away goals) | |||
| Niger | 2-0 | Guinea | (2-1) |
| Togo | 2-1 | Gabon | (3-2) |
