The Super Eagles had to come from behind in Uyo to edge past neighbours Benin 2-1 in Group L.
Veteran forward Stephane Sessegnon scored the opener for the Squirrels after just three minutes as he took advantage of some poor defending to put the ball past Nigeria keeper Daniel Akpeyi.
The Super Eagles then came close on 40 minutes as Villareal’s Samuel Chukwueze hit the woodwork.
Nigeria drew level in injury time at the end of the first half when Victor Osimhen scored from the penalty spot to continue the form he has been enjoying at French side Lille, where he has scored nine goals this season.
The referee awarded the spot kick after a foul on Torino’s former Chelsea player Ola Aina.
Bordeaux’s Samuel Kalu sealed the win just past the hour mark as he dribbled into the area to score from close range.
In the other Group L game Sierra Leone and Lesotho drew 1-1 as both sides finished with 10 men.
Iceland-based Kwame Quee scored for Sierra Leone in an empty stadium in the 69th minute to give the hosts the lead.