The match ended 1-1 after extra-time and Nigeria claimed the penalty session 4-2. Extra-time substitute Kelechi Iheanacho drove home the decisive kick.
The 27-year-old Leicester City forward - once touted to become an illustrious international marksman - has been eclipsed by Victor Osimhen and had not featured in the tournament before his introduction after 102 minutes of the semi-final.
He ripped his shirt off and sprinted to the Nigeria fans at the other end of the stadium as he revelled in his moment as his nation's saviour.
But for Ademola Lookman's clumsiness, Iheanacho would not have had the chance to shine.
Lookman could have wrapped up the tie in the 85th minute as South Africa sought an equaliser. But the Atalanta striker tried to take the ball round the South Africa goalkeeper Ronwen Williams and was thwarted.
In the prelude to the game at the Stade de la Paix, the Nigeria boss José Peseiro cracked down on the idea that his side would be favourites for the tie.
And the 63-year-old's caution was vindicated during an opening half in which his charges were forced to run after the ball and South Africa monopolised the chances.
A ricochet took the ball to him 15 metres from goal but the Al Ahly striker snatched at his shot and it trickled tamely to Nwabali
A heavy touch betrayed Tau a few minutes later as he outsprinted Ajayi Adesewo down the left and bore down on goal.
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