Nigeria are still top of Group C in the Africa zone of the 2022 World Cup qualifying series.
The Super Eagles suffered a shock 1-0 loss to Central African Republic on Thursday.
Karl Namnganda netted the winner for the Wild Beasts in the 90th minute of the encounter at the Teslim Balogun Stadium in Lagos.
Gernot Rohr’s men now have six points from three matches
Earlier in the day, Cape Verde fought back from a goal down to defeat Liberia 2-1 at the Ohene Djan Sports Stadium, Accra.
They are level on four points with CAR, while Liberia are now at the bottom with three points.
Nigeria travel to Central African Republic for the reverse fixture in Douala on Sunday.