Teboho Mokoena handed Matsatsantsa an early lead, but second-half goals from Zakhele Lepasa and Tshegofatso Mabasa inspired the Buccaneers to a hard-fought victory.
The Buccaneers were looking to record their fourth successive win across all competitions having brushed aside Kaizer Chiefs 2-0 in the MTN8 semi-final second-leg match just before the Fifa break.
Coach Josef Zinnbauer named an unchanged team with Thulani Hlatshwayo leading the Soweto giants, while Deon Hotto, who was named Man of the Match after the win over Chiefs, kept his place in the starting line-up.
Meanwhile, Matsatsantsa were keen to bounce back to winning ways after crashing out of the MTN8 following a 1-0 defeat to Bloemfontein Celtic in the semi-final second-leg encounter on November 7.
Zinnbauer's counterpart, Kaitano Tembo made five changes to the team which faced Celtic with Sipho Mbule, Evans Rusike, Luke Fleurs, Iqraam Rayners and Grant Kekana all making their return to the starting line-up.
SuperSport got off to the perfect start as they broke the deadlock just six minutes into the match after the Pirates defence was caught ball watching in the box.
Rusike's tame shot found an unmarked Teboho Mokoena in the box and the young midfielder turned and beat Bucs goalkeeper Richard Ofori with a low effort to make it 1-0 to SuperSport.
Pirates then took control of the match with the visitors happy to sit back and launch quick counter-attacks with the likes of Rusike and Rayners looking to use their speed to cause havoc for the hosts' defence.
Ronwen Williams was the busier of the two keepers as he produced a fine save from Ntsikelelo Nyauza's header, before coming out to gather Hotto's through pass which was meant for Vincent Pule.
With the half-time break fast approaching, Matsatsantsa's defence was solid and compact which saw Bucs resorting to long-range shots which did not trouble Williams in the visitors' goal-posts.
The score was 1-0 to SuperSport at the interval courtesy of the in-form Mokoena's third league goal of the current campaign.
Pirates piled more pressure on the visitors after the restart and the hosts were awarded a penalty when Zakhele Lepasa was fouled by Siyabonga Nhlapo in the box.
New South Africa under-23 international Lepasa then dusted himself down to convert the penalty - making it 1-1 six minutes into the second half.
SuperSport changed their approach after conceding as Tembo introduced attack-minded Ghampani Lungu and the visitors pushed forward in numbers as they looked to regain the lead.
Mokoena forced Ofori into a comfortable save with a long-range shot, before Bradley Grobler and Mbule placed their efforts wide of the target in the closing stages of the match.
Zinnbauer reacted by introducing Linda Mntambo, who came off the bench to score for Bucs in their victory over Chiefs on November 8 at FNB Stadium, and fit-again Tshegofatso Mabasa.
The move paid off as Mabasa grabbed a late winning goal in the 87th minute when he fired home from close range after some good work by Innocent Maela, who had nutmegged Williams.
The 2-1 victory took Pirates to the top of the league standings - a point above defending champions Mamelodi Sundowns, while SuperSport remained sixth on the table.