Second half goals from Thabo September and Kermit Erasmus sealed the win, after Sundowns had Clayton Daniels red-carded in the 17th minute for a tackle on Erasmus.
The victory is SuperSport’s third in the Nedbank Cup competition, but their first since they beat BidVest Wits in 2005 final.
It is also the second win in the competition for coach Gavin Hunt, who lead Moroka Swallows to a 3-1 success over Manning Rangers in 2004.
As early as the eight minute SuperSport were twice denied the lead by the brilliance of Sundowns goalkeeper Wayne Sandilands.
Thabiso Nkoana skilfully cut in from the right wing and forced a good save off Sandilands and then from the rebound ball Nkoana crossed for Sibusiso Zuma who was also denied by the Bafana Bafana shot stopper from six-yards.
The match’s most important moment came in the 17th minute when Sundown’s centre half Daniels was shown a straight red card for bringing down Erasmus outside the box.
Matsatsantsa then made the extra man count when September lost his markers and met Sahmeeg Doutie’s corner kick and headed home at the far post.
The Brazilians started the second stanza in a spirited mood and could have equalised in the 52nd minute when Modise attempted a right footed shot just outside the box that went agonisingly over the bar.
But in the 60th minute, all Sundowns’ momentum was killed when United grabbed their second goal, which effectively closed out the match.
Zuma played found an unmarked Erasmus and his first shot was saved by Sandilands from close range, but he did not need a second invitation when he coolly lobbed the rebounded ball into an empty net.
The Brazilians tried by all means but could not do enough to keep the match alive as Matsatsantsa won their first ever cup trophy under triple League winning coach Gavin Hunt.
The Nedbank Cup Final line-ups:
SuperSport: Ronwen Williams, Morgan Gould, Thabo September, Moffat Mdluli (Hartog 58'), Davis Nkausu, Tebogo Langerman, Edwin Gyimah, Sibusiso Zuma (Khenyeza 80'), Kermit Erasmus (Gabonamong 74'), Sameehg Doutie, Dipsy Selolwane.
Sundowns: Wayne Sandilands, Clayton Daniels, Siyanda Xulu, Method Mwanjale, Punch Masenamela, Surprise Moriri (Nyandoro 65'), Teko Modise, Elias Pelembe (Mphela 66'), Hlompho Kekana, Nyasha Mushekwi, Lebohang Mokoena.