Towering striker Sthembiso Ngcobo got the goal on 21 minutes to hand United their first defeat of the season.
The Clever Boys started slowly but eased their way into the challenge while the Team of Choice looked shaky in defence.
A mistake at the back after 20 minutes allowed Ngcobo a look-in at goal and before long, the attacker put the home side ahead with a toe-poke after a mix up between goalkeeper Shu-Aib Walters and his defensive line.
United struggled to adjust and were forced into an early substitution as striker Deolin Mekoa was sacrificed in order for a more defensive Philani Zulu.
United were clearly rattled by the early goal and the Clever Boys continued to mount serious pressure.
Ngcobo had a host of chances and looked in good shape, but for a resilient Walters, who atoned for his error with several good blocks before the end of the half.
Trailing at the interval, United did little to improve their prospects and looked in danger of leaking a few more.
Ngcobo headed wide twice in two minutes when a goal looked more likely, but Wits were clearly the only team on the field.
United's defence stood firm and absorbed plenty of pressure as Wits looked relentless in attack, searching for a second.
Maritzburg had undoubtedly their best chance of the game to that point fall to Ashley Hartog, who rattled the upright with a hammer blow on 75 minutes.