The hosts took the lead when Ronwen Williams scored an own goal following a defensive mix-up in the box, but two goals from Bradley Grobler inspired Matsatsantsa to a victory.
The Team of Choice were desperate to snap their six-match losing run in the league after succumbing to a 1-0 defeat to Black Leopards in their match last weekend.
Assistant coach Delron Buckley, who was in charge of the team in the absence of Ernst Middendorp, recalled Thabiso Kutumela to the starting line-up after the striker was benched against Leopards.
Meanwhile, Matsatsantsa were hoping to avoid their third successive defeat after suffering a 2-1 loss to Orlando Pirates in their previous match last weekend.
Coach Kaitano Tembo made three changes to the team which faced Pirates with Ghampani Lungu, Kudakwashe Mahachi and Thatayaone Ditlhokwe making their return to starting line-up.
Maritzburg got off to a bright start with Kutumela causing havoc for the SuperSport defence with his clever movement in the visitors' half.
The deadlock was broken just eight minutes into the match after Kutumela's low shot was brilliantly saved by SuperSport goalkeeper Ronwen Williams.
However, Onismor Bhasera's attempted clearance hit Williams and the ball went into the back of the net to make it 1-0 to Maritzburg.
Matsatsantsa then took control of the match and they managed to restore parity after some good work by Evans Rusike down the right-hand side beating two defenders.
The Zimbabwe international then set-up Grobler, who made no mistake as he beat Maritzburg keeper Sebastian Mwange to make it 1-1 in the 14th minute.
The visitors came very close to making it 2-1 when Lungu was sent through on goal and he rounded Mwange, but his effort was brilliantly cleared off the goal-line by Daniel Morgan.
Mahachi had a chance to hand Matsatsantsa the lead just before half-time, but he was denied by Mwange, who ensured that the first-half ended with the two teams locked at 1-1.
Maritzburg dominated possession after the restart, but they were struggling to create goalscoring opportunities with the SuperSport defence looking impenetrable.
The visitors took the lead for the first time on the night against the run of play when Mahachi combined with Grobler, who fired past Mwange to make it 2-1 to SuperSport in the 64th minute.
The momentum was with the Team of Choice in the closing stages of the match with Williams producing a magnificent finger-tipping save to deny Judas Moseamedi.
Bongokuhle Hlongwane and Fares Hachi were both introduced by Buckley as the home side looked to snatch a late equalizing goal.
However, SuperSport stood firm at the back in the dying minutes of the match and ultimately, they secured a hard-fought 2-1 victory over Maritzburg.
The victory took Matsatsantsa to the third spot on the league standings, while the Team of Choice remain 16th on the table.