Imrana Muhammad gave Nigeria the lead in the ninth minute.
The Black Starlets fought back, with Harve Gbafa netting the equaliser 10 minutes later.
Gbafa scored his second goal of the game three minutes before half hour mark, capitalising on an error by a Nigerian defender.
Nigeria levelled four minutes before the break following a superb attacking play.
Abdulmuiz Adeleke nodded home from a John Ogwuche cross.
Adeleke fired home the winning goal two minutes into stoppage time.
The young forward finished the competition with four goals.