Two second half goals from Umar Sadiq and captain William Troost-Ekong edged Nigeria above Guinea-Bissau on Wednesday at the 2021 AFCON in Cameroon.
Sadiq found the back of the net in the 56th minute through a Kelechi Iheanacho assist. Troost-Ekong made it 2-0 in the 75th minute at Roumde Adjia Stadium.
The Super Eagles have now finished top of the group on nine points while Egypt followed in second place on six points after defeating Sudan 1-0 on Wednesday.
Guinea-Bissau held off Nigeria to a goalless draw in the first half.
The Super Eagles went into the match with significant changes in the squads that defeated Egypt and Sudan.
Iheanacho, Wilfred Ndidi and Troost-Ekong however maintained their places in the team.
The Omonoia Nicosia goalkeeper Francis Uzoho got the nod to start while Maduka Okoye was rested after playing the last two games.
The other starters included defenders Jamilu Collins, Semi Ajayi and Tyronne Ebuehi, midfielders Alex Iwobi, Kelechi Nwakali and Chidera Ejuke, and forward Umar Sadiq.