Defender William Troost-Ekong, gave the Nigerian team a 1-0 lead from the penalty spot in the 55th minute after striker Victor Osimhen was bundled by Ivorian defenders in the penalty box.
The Eagles matched the firepower of the host country in the game which was a contrasting performance from the one against Equatorial Guinea on Sunday.
Before the goal, both teams had their chances, with the Nigerian team being the most wasteful in front of goal.
