In a game that Baroka bossed throughout captain Olaleng Shaku bagged a first half goal and Mduduzi Mdatsane sealed it inside the final 10 minutes at Peter Mokaba Stadium.
Baroka had the advantage early in the game as a set-piece delivered in by Mdatsane was met brilliantly by the head of Shaku who had run from deep to avoid being picked up by the defence.
Other than the goal it was a first-half largely devoid of chances of real consequence with Stellenbosch, despite being behind, creating very little up front.
Midway through the half assist provider Mdatsane fired a free-kick straight down the throat of Washington Arubi.
Moments before the interval the Zimbabwean stopper was called into action again as neat interplay availed the ball to Mdatsane in the box and he tried to nudge it past Arubi only to have his effort smothered.
Coming out of the break Baroka went in search of a cushion and Victor Letsoalo fired a free kick wastefully over whilst Letladi Madubanya saw his fierce low drive handled by a well-positioned Arubi.
The home side continued to create chances and Stellenbosch captain Junaid Sait was forced to clear off the line as Letsoalo beat Arubi to a ball over the top and lobbed it towards goal.
Bakgaga had an opportunity to seal the game in the 80th minute as Letsoalo found himself alone in the box with only Arubi to beat but his unconvincing shot came back off the upright.
Minutes later Mdatsane found himself in an almost identical position and similarly his shot hit the post but this time went in to wrap things up for Baroka.
The victory leaves the Limpopo side on seven points whilst Stellenbosch, with two, are out of the running entirely.
Baroka: Masuluke, Mahashe, Kgoetyane, Shaku, Masenamela, Madatsane (Matlakala 90+5), Madubanya, Moeti (Maleka 73'), Letsoalo, Matloga, Kgaswane (Mapheto 90+2')
Stellenbosch: Arubi, Lecki, Rowell, Sait, Hadebe (Adonis 44'), Booysen (Webber 65'), Mekoa, Moroole, Muishond, More, Niang (Dube 62')