The Super Eagles beats Sierra Leone 3-2, while Guinea-Bissau won 1-0 at Sao Tome and Principe.
Zambia joined South Africa as another COSAFA nation going to the finals.
Equatorial Guinea and Egypt also qualified on Matchday 5.
While Ivory Coast booked their place at the finals tournament as hosts, while defending champions Senegal, Morocco, Algeria, Burkina Faso and Tunisia completes the list.
A total of 24 teams will qualify to play in the final tournament.
And Sao Tome and Principe, Botswana, Lesotho and Madagascar, Libya, Liberia, Comoros, South Sudan, Ethiopia, are already out of the tournament.