The hosts started well as they looked to continue the impressive run they have had in the early stages of their league campaign.
Haashim Domingo had the first real chance of the game just after the half-hour mark when he controlled well but sent his volley flying just over the crossbar from inside the area.
The Clever Boys looked menacing as SuperSport struggled to deal with Deon Hotto, Mxolisi Macuphu and Domingo going forward, their movement, pace and combinations proving too much to deal with in most instances.
The visitors created their first real opening just before the end of the first half. Aubrey Modiba smashed his effort over the crossbar from the edge of the area though.
The sides went into the break level but with Bidvest Wits buoyed by their first half showing.
Coach Gavin Hunt introduced Bantu Mzwakali at the start of the second half in place of Hotto as the Braamfontein outfit looked for their fourth straight win.
The pace slowed in the second half, with both sides struggling to find their rhythm or put together meaningful combinations in the midfield.
With 19 minutes remaining SuperSport broke the deadlock through Evans Rusike who latched on to a deflected Onismor Bhasera shot and was able to direct his volley past Darren Keet.
The goal saw Wits spring to life and push for a point, but Matsatsantsa were able to keep the Wits attack at bay and hold on for a vital three points.
The result sees SuperSport move into third position on the log while Wits remain at the summit for the time being.
The Clever Boys will be looking to course-correct when they face AmaZulu on 29 August at the Bidvest Stadium, kick off is set for 19:30.