The West African nation collected seven points in the initial stage thanks to their two wins and a draw.
Nigeria then claimed a huge 5-0 victory over Zambia in the quarter-final.
It was the same case in the initial stage for the defending champions, who secured seven points in their pool to advance.
Banyana Banyana's quarter-final game was decided on penalties following a goalless draw in both regulation and extra time. Desiree Ellis' team won 4-1 to set a date with the Super Eagles.
In the head-to-head record, this is the 12th WAFCON meeting between the nations; in the previous 11 engagements, the Super Falcons have managed seven wins, with Banyana Banyana securing just three, while the remaining fixture ended in a draw.
The last meeting was in 2022's Group Stage, where South Africa claimed a 2-1 win en route to their maiden continental crown.
It will be the fifth time South Africa and Nigeria are meeting in the semi-final: 2002, 2012, 2014, and 2016. The Super Falcons won 5-0, lost 1-0, and then managed 2-1 and 1-0 wins, respectively.