The win was a second in three weeks for the Students over Matsatsantsa, and sees the league champions climbing further away from the relegation zone as they moved up to 12th position and four points clear of the drop zone.
SuperSport, meanwhile, are only above Wits on goal difference and have won just one of their last 12 league matches.
The first half brought little in the way of goal mouth action as the two sides cancelled each other out in midfield.
The only real noteworthy action up front led to the opening goal when Wits skipper Thulani Hlatshwayo mis-timed his attempt to clear a cross and handled the ball, albeit unintentionally.
SuperSport captain Dean Furman stepped up to the spot and placed a crisply-struck penalty past the out-stretched arms of Darren Keet to give the Tshwane team the lead midway through the first half.
Having come close to doubling their lead just after half time when Kingston Nkhatha crashed a volley against the woodwork, Matsatsantsa instead found the game back on level terms in the 47th minute when some sloppy defending allowed a cross to reach Gabadinho Mhango, who fired home from 12-yards out.
The Clever Boys went in front for the first time in the match just five minutes later when James Keene used his muscle to head in from a Sifiso Myeni corner.
It got worse for Eric Tinkler’s SuperSport side in the 64th minute when Daylon Claasen drilled in a thunderous drive from outside the area after he had been teed up by Mhango, the Bafana Bafana international registering his first goal for Wits in style.
The home team were a little unlucky not to pull a goal back soon after when Aubrey Modiba’s cross hit the bar.
For the most part though Gavin Hunt’s Students remained firmly in control, looking more like last season’s league-winning outfit and there was even time for Hlatshwayo to make amends for his earlier mistake when he powered in a header from a Myeni cross in the 87th minute to complete SuperSport’s misery.
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