Nigeria beat the half-time whistle to take the lead when captain Rasheedat Ajibade beat Andile Dlamini from the penalty spot after Karabo Dhlamini had been adjudged to have handled inside the box.
But Banyana got themselves back into the game on the hour mark, also via a penalty when Osinachi Ohale pulled down Hildah Magaia inside the box and Linda Motlhalo took the responsibility to score.
Motlhalo's goal saw the West Africans conceding for the first time in this tournament edition.
As the game seemed headed to extra-time, the Super Falcons reclaimed their lead in stoppage time when Michelle Alozie sent in a fricky cross, which two forwards failed to finish as the ball went straight into the back of the net.
It then ended 2-1 in favour of Nigeria, who remain on course for a 10th WAFCON title.