Their win sees Wits leapfrog into second place in the standings while the Port Elizabeth team currently languishes in sixth position.
The two sides had gone into the second round with one point each, after both had notched up goalless draws in their opening fixtures.
However, Madibaz head coach Graeme Harrison remained positive, saying the result was not an accurate reflection of his squad’s performance.
“It was a very close game and I wouldn’t say that Wits necessarily dominated us,” said Harrison.
Wits substitute Graeme Dor managed to open the scoring midway through the second half to secure the win for the Johannesburg team.
“It was just one of those games where we couldn’t find our rhythm. We couldn’t get past their defence and the ball just didn’t roll for us,” said Harrison.
The visitors’ confidence was also dealt a blow when star striker Kieran Koert was sidelined within the first five minutes with a shoulder injury.
He said although things had not come together as planned on Monday night, his players were ready to come back fighting next week.
Harrison added that it was still early days and that the Madibaz had a number of chances to move up on the log.
He said the team would focus on their attacking play ahead of next week’s game.
The Madibaz are set to take on the University of Pretoria in the third round of the Varsity Football tournament at the Tuks Sport Stadium in Pretoria at 5pm on Monday night.
For more news see Varisty Football.