Sundowns Ladies coach Jerry Tshabalala made two changes from the side that drew with FAR Rabat the last time out, as Melinda Kgadieta and Lelona Daweti were recalled.
Banyana Ba Style, who were the only side not to concede in the group stages, were showing their defensive nous in the opening exchanges, denying Malabo any sight of goal.
Tshabalala's ladies had the flair going forward and they carved out their first chance in the 20th minute after Precious Morifi cut inside the box from the wing and unleashed a strike that was saved by goalkeeper Ruth Sunday.
However, Sundowns Ladies were being shut out in the closing phase of the first stanza, as the Equatoguinean side were getting physical and the first stanza ended without goals.
The South African side were finding joy in the last third coming from the half-time break, keeping Sunday busy in goal and Daweti came close to breaking the deadlock on the hour-mark with a strike that hit the post after a square pass by Morifi.
Banyana Ba Style were putting Malabo under pressure but not finding openings and with 18 minutes remaining, Tshabalala brought on Andisiwe Mgcoyi in place of Rhoda Mulaudzi for fresh legs upfront and the move nearly paid off, as Mgcoyi had a chance with a header ten minutes before time that sailed over the bar.
Sundowns kept on threatening for that elusive goal but they were not finding a way through a reinforced defence and the match went to extra-time after ending goalless in regulation time.
Banyana Ba Style continued to dominate Malabo in extra-time, with shot-stopper Andile Dlamini not having much to do but they lacked the finishing touches in front of goal.
Malabo were defending deep, forcing Sundowns Ladies to have long range strikes and Thalea Lauren came close to snatching the winner for the South African side two minutes before time with a strike from outside the box that hit the woodwork and had another shot from the rebound that was saved by Sunday.
The match eventually went to penalty shoot-outs, where Sundowns claimed a 5-4 win with Bongiwe Thusi scoring the decisive kick in sudden-death to set up a final against Hasaacas Ladies of Ghana on Friday evening.