Detailed explanation of the seeding method.
The third place match won't affect the final ranking, as both Nigeria and Algeria will remain with 6 bonus points - as semifinalists.
It's between Ghana and Egypt - whoever wins the final, will also be in Group 1, as both teams are tied on 31 points.
The rest of the groups (from 3 through 13) are already set in stone if CAF will use the same system as in 2006.
Group 1: Egypt/Ghana, Congo, Madagascar, Sao Tome e Principe
Group 2: Ghana/Egypt, Cape Verde Islands, Lesotho, Central African Republic
Group 3: Nigeria, Gambia, Burundi, Guinea-Bissau
Group 4: Algeria, Senegal, Chad, Djibouti
Group 5: Côte d'Ivoire, South Africa, Swaziland, Somalia
Group 6: Cameroon, Uganda, Sierra Leone, Mauritius
Group 7: Tunisia, Sudan, Ethiopia, Seychelles
Group 8: Mali, Rwanda, Botswana, Comoros
Group 9: Burkina Faso, Kenya, Zimbabwe, Eritrea
Group 10: Zambia, Guinea, Libya, Niger
Group 11: Benin, Morocco, Congo DR, Mauritania
Group 12: Angola, Malawi, Namibia, Liberia
Group 13: Mozambique, Togo, Tanzania
I apreciate the effort made by an unregistered Wikipedian on the 2012 Africa Nations Cup qualification article, but I don't think this info should be on Wikipedia as it's not yet official.
According to an e-mail I received from CAF no team has withdrawn from the qualifiers. Probably some teams will withdraw after the groups are announced.
CAF could also choose a system with 14 groups - only the winners advacing to the 2012 ACN. However, they had a similar option in 2006. 47 teams and 15 available places - 13 groups of 3 geams and 2 of 4 teams, with only the winner advancing. Instead they chose the system that would have the most groups with 4 teams.
Anyway, this is how the groups would look like in a 14-group setup:
Group 1: Egypt/Ghana, Namibia, Niger, Sao Tome e Principe
Group 2: Ghana/Egypt, Tanzania, Mauritania, Central African Republic
Group 3: Nigeria, Congo, Liberia, Guinea-Bissau
Group 4: Algeria, Cape Verde Islands, Madagascar, Djibouti
Group 5: Côte d'Ivoire, Gambia, Lesotho, Somalia
Group 6: Cameroon, Senegal, Burundi, Mauritius
Group 7: Tunisia, South Africa, Chad, Seychelles
Group 8: Mali, Uganda, Swaziland, Comoros
Group 9: Burkina Faso, Sudan, Sierra Leone, Eritrea
Group 10: Zambia, Rwanda, Ethiopia
Group 11: Benin, Kenya, Botswana
Group 12: Angola, Guinea, Zimbabwe
Group 13: Mozambique, Morocco, Libya
Group 14: Togo, Malawi, Congo DR