A debut for Antonio Van Wyk headlined the home side's eleven with Nathan Sinkala introduced too, whilst United started Bradley Grobler and named Thamsanqa Gabuza on the bench.
The Tshwane side threatened within the opening two minutes through an attempt from a tight angle by Ghampani Lungu, but he went wide with the resultant effort.
Stellenbosch launched their first chance from a free-kick by Ashley Du Preez after a few minutes from the start, but the attempt didn't trouble goalkeeper Ronwen Williams.
Matsatsantsa pulled a response before the half-hour mark when Jamie Webber's ball from a set-piece connected with Kegan Johannes, who headed the delivery wide from an unmarked position.
Another opportunity from a free-kick this time came Webber's way minutes to halftime, but Stellies goalkeeper Sage Stephens parried the midfielder's plight.
SuperSport were close to the lead again moments following the restart when Iqraam Rayners headed a cross from Moses Waiswa against the woodwork.
The Maroons and Whites began to reclaim dominance as the second period began to open up and were inches away from the lead through Du Preez, but United's rear-guard smothered.
Matsatsants put on a fresh pair of legs in the closing exchanges, with Selaelo Rasebotja withdrawn and Jesse Donn introduced.
It was SuperSport that enjoyed the lion share of chances late on and as such grabbed the winner courtesy of a close-range finish by Grobler that denied Stellies a point.
Stellenbosch: Stephens, Kwinika, Mcaba, Van Rooyen, Letsoenyo, Sinkala, Jabaar, Van Wyk, Dimgba, Du Preez, Mendieta.
Subs: Bombay, Johannes, Adams, Isaacs, Johannes, Khunyedi, De Goede, Moseamedi, Van Heerden, Scott.
SuperSport: Williams, Nhlapo, Johannes, Ditlhokwe, Bhasrea, Waiswa, Rasebotja, Webber, Rayners, Lungu, Grobler.
Subs: Pule, Phillips, Donn, Moralo, Gabuza, Fleurs, Appollis.