The Super Eagles lost 2-0 in their final Group B fixture against Madagascar on Sunday.
This means Nigeria finished in second place with six points, behind the debutants who got seven points.
Gernot Rohr’s men had already qualified for the Round of 16, following their back-to-back 1-0 wins over Burundi and Guinea and were looking to seal top place.
However, as runners-up, they will now face the team that finishes second in Group F.
Currently, Cameroon lead with four points after two games. Ghana and Benin occupy second place with two points, while Guinea-Bissau have only one point.
The final round of fixtures on Tuesday, July 2, will see Benin take on Cameroon and Ghana play Guinea-Bissau.
As it stands, Nigeria could face any of the four teams from Group F, as no position is confirmed yet.