The Eagles came into the final group game with a plan to emerge group leaders while the Guinea-Bissau side came intending to secure their first-ever AFCON victory.
Guinea Bussau’s Opa Sangante diverted Moses Simon’s dangerous cross into his own net to give Nigeria a first-half lead in the 37th minute.
Equatorial Guinea’s 4-0 win over hosts, Ivory Coast have placed them 1st in the group while Nigeria stays in second place.
With today’s matches, Group A teams, Nigeria and Equatorial Guinea with 7 points each have qualified for the knockout stage while host Cote d’Ivoire and Guinea Bissau have been eliminated.