Desire Oparanozie was the match winner for the defending champions when her hugely deflected free kick in the 54th minute proved to be the difference between the two teams.
South Africa had a goal chalked off in the first half for offside, otherwise Nigeria dominated with the magical Ngozi Okobi and skipper Rita Chikwelu pulling the strings in midfield.
Late in the game, Ugo Njoku almost caused an own goal but goalkeeper Alaba Jonathan was alert to keep out the danger, before Faith Ikidi made two goal line clearances in quick succession as Banyana Banyana poured forward in a bid to draw level.
Saturday’s final will be a repeat of the 2014 championship game in Namibia which Nigeria won 2-0 at the expense of the Cameroonians.
Ghana and South Africa will play the third-place game on Friday.