The Nigerians opened the scoring through Troost-Ekong (38th), while Franck Kessié equalized for Côte d'Ivoire (63rd). Sebastien Haller scored the winner with nine minutes of normal time remaining.
This is the third trophy for Côte d'Ivoire after their 1992 and 2015 triumphs.
In the semi-finals, held last Wednesday, Côte d'Ivoire eliminated DR Congo (1-0), while Nigeria beat South Africa on penalties (4-2 /1-1 in normal and extra times).
On Saturday, South Africa won the match for third place against DR Congo (6-5 on penalties, 0-0 regulation time).