Thulani Hlatshwayo scored the only goal of the game in the 74th minute.
Both keepers were forced into early saves, with Ronwen Williams doing well to deny Henrico Botes in the 13th minute, before Moeneeb Josephs kept out a David Mathebula free-kick.
Wits had a string of opportunities around the half-hour mark, with Siyabonga Nhlapo, Sibusiso Vilakazi and then Botes going close to finding the back of the net.
Both teams were also guilty of missing sitters on the cusp of half-time. Ben Motshwari sent his shot off target with the goal at his mercy, before Dove Wome failed to find the back of the net from point-blank range with Josephs off his line.
SuperSport suffered a major blow in first-half stoppage time with Dumisani Msibi replacing the injured Ronwen Williams, who had to be carried off on a stretcher following a collision with Sameehg Doutie. It was Msibi’s debut.
The Clever Boys dominated the early exchanges of the second stanza, with Josephs a mere spectator between the sticks.
And they finally found the opener in the 74th minute. Hlatshwayo evaded his marker before heading past Msibi from a pin-point Phumlani Ntshangase corner-kick.
Mathebula and Thabo September went close to leveling matters soon after. Mathebula forced Josephs into a good save, before September saw his header flash wide of the right-hand post.
Wits held on to move within 13 points of Kaizer Chiefs, while SuperSport United remain in 12th spot.