Siyanda Xulu returned from injury with Jeremy Brockie, who scored to rescue a point against Cape Town City. Meanwhile, Asavela Mbekile and Nathan Sankala made their debuts for the home side.
Leletu Skelem could've given Stellies a fifth-minute lead after getting on the end of Ovidy Karuru's cross on the right, but the attacker fired wide from the back post.
Stellies did however manage to go in front three minutes later after Mpho Matsi capitalised on sloppy goalkeeping from Bongani Mpandle to slot home from close-range.
The Team of Choice levelled from the spot on 22 minutes after Thabiso Kutumela sent Boy de Jong the wrong way following a foul on Tebogo Tlolane inside the six-yard area.
Stellies needed only four minutes to regain the lead as Skelem atoned for his earlier miss to turn home a loose ball from a goal-mouth scramble following a throw-in.
Ryan Moon looked to give Stellies a third on 34 minutes, but Mpandle parried his header behind for a corner following a pin-point cross.
Neat one-two touches around the area from United ended with Kutumela, who arrived on the near side to drill into the top corner to restore pairty once again a minute before halftime.
Yusuf Jappie came on for the visiting side following the start of the second half, as full-back Daniel Morgan made way for the winger.
Stellies should've gone back in front following the 61st minute, but Moon volleyed over the top with a clear sight on goal.
Both sides pushed to regain the lead afterwards, but poor attacking interplay from either side took the encounter to extra time.
The extra minutes yielded no goals and the two sides went into a penalty shoot-out, which went the way of the Team of Choice after Stellies missed four kicks.
Stellenbosch: De Jong, Mobbie, Ndlovu, Mthethwa, Johannes, Mbekile, Sinkala, Matsi, Skelem, Karuru, 29. Moon.
Subs: Pool, Gould, Rayners, Bergman, Scott, Isaacs, Mathabela.
Maritzburg: Mpandle, Morgan, Xulu, Mngonyama, De Reuck, Kutumela, Timm, Claasen, Ntshangase, Tlolane, Brockie.
Subs: Barr, Allie, Kunene, Buchanan, Shandu, Augusto, Jappie.