These two sides met in the group stage phase, with Desiree Ellis' charges running out 1-0 winners a fortnight ago.
The Super Falcons had the first meaningful effort at goal in the opening stages, but goalkeeper Kaylin Swartz pulled off the save at the second time of asking after spilling.
Swartz was certainly the busier of the two goalkeepers as she came to Banyana's rescue with a superb save in the 24th minute as Nigeria threatened.
The Super Falcons went close once again in the 37th minute through Ordega Francisca, who saw her curling effort fly just wide of the target.
Upon resumption in the second half, Asisat Oshoala was quite lively for the Falcons down the flanks, but chances were still hard to come by for her side.
Oshoala had the chance to be a hero when Nigeria were awarded a penalty in the 74th minute, however the Falcons striker placed his effort wide of the mark.
Chances were hard to come by for both nations in the remaining stages of regulation time, which ultimately sent the clash to extra-time.
After both sides failed to break the deadlock in the extra 30 minutes, it was left to a penalty shoot-out and it was the Falcons who came out victorious to claim the title.