The match had ended 0-0 after 120 minutes, with Nigeria’s goalkeeper Tochukwu Oluehi making the trophy-winning save in the shoot-out from the boot of South Africa’s Linda Motlhalo.
Experienced midfielder Asisat Oshoala had earlier scuppered the chance to seal a victory for Nigeria in normal time after she missed a penalty.
The Super Falcons, who came to Ghana as defending champions, retain their dominance in this competition, winning the trophy for a ninth time in eleven editions.
South Africa looked the more purposeful pushing forward, but the Nigerian defence dealt with the attacks comfortably.
Mamemlo Makhbane’s long range strike for Banyana Banyana in the 12th minute had to be palmed wide by Nigeria’s keeper, as South Africa began to impose themselves on the game.