Mercy Tago's ladies made a fine start to the game as Mukarama Abdulai dashed into the area to shoot but Evelyn Nwabouku made a block to divert it behind for a corner.
With Ghana failing to capitalise on their early chances in the opening 15 minutes, Nigeria came alive and almost found an opener through Rafait Sule in the 33rd minute.
In the second half, both teams missed several scoring chances and neither side could find the back of the net before the end of regulation time.
It took kicks from the penalty mark to separate both teams as the Super Falcons avenged last edition's semi-final defeat to the Black Queens.
For Ghana, it was a disappointment as they failed in their quest to defend the title they won last year.
Earlier, Ange Koko N'Guessan and Mariam Diakite were on target as Cote d'Ivoire secured a 2-1 comeback semi-final win over Mali to reach the final.
On Saturday, Ghana will take on Mali in the third-place final, before hosts Cote d'Ivoire battle Nigeria for the title.