Bandile Shandu and Nazeer Allie were recalled to the Maritzburg side from the 1-1 draw against Baroka FC, as Stellies restored Leletu Skelem to the playing personnel.
Zambian Nathan Sinkala looked keen to open the deadlock inside the first 20 minutes from a corner-kick, but his header sailed over the crossbar from close range.
Ashley Du Preez missed a big chance from a defensive error ten minutes to halftime to put the host ahead, as he miscued a loose ball and resultantly let the chance slip.
Maritzburg began to come alive barring the slow spell and missed a big chance to take the lead from the back-post by Travis Graham a little later following Bongokuhle Hlongwane's cutback.
Although momentum soon returned to Stellies and had Du Preez on the end of a ball in behind the defence, but goalkeeper Marcel Engelhardt thwarted before Skelem fluffed the follow-up.
The Team of Choice entered the second half keen to revitalise their stall following a slow first half, but a bewildered Stellies didn't back down with Daniel Morgan and Fares Hachi introduced.
Stellies could've finished off matters late on from a move across the area, but Phathutshedzo Nange and Sinkala couldn't pounce.
Matters however turned in added time after a handball from Junior Mendieta gave Maritzburg a penalty, which Thabiso Kutumela converted for the three points that keeps them in 13th spot.
Stellenbosch: Stephens, Macheke, De Goede, Mthethwa, Van Heerden, Van Rooyen, Jabaar, Sinkala, Du Preez, Adams, Skelem.
Subs: Langeveldt, Mbekile, Robertson, Brenner, Scott, Nange, Mendieta, Msengi, Avontuur.
Maritzburg: Engelhardt, Claasen, Kutumela, Daniels, Tlolane, Rae, Allie, Graham, Stevic, Hlongwane, Shandu.
Subs: Barr, Hlubi, Moseamedi, Morgan, Modise, Ismail, Sifama, Hachi, Ntshangase.