The Citizens were looking to keep the momentum going after thrashing Free State Stars 5-0 in their last match in the league.
Meanwhile, Matsatsantsa were looking to get the better of City, who had beaten them three times already this season - twice in the Absa Premiership and in the MTN8 Final via penalties.
The game got off to a quiet start with regards to chances, but Thato Mokeke eventually broke the deadlock for Benni McCarthy’s men in the 36th minute with a header from six-yards out.
SuperSport, meanwhile, found it tough to breakdown the City defence as striker Bradley Grobler cut a frustrated figure upfront.
Thamsanqa Mkhize doubled the lead for City four minutes before the hour with a low strike inside the box that took a deflection and wrong footed goalkeeper Ronwen Williams after some good work by Ayanda Patosi.
United were looking for fresh legs after the hour-mark as veteran midfielder Reneilwe Letsholonyane made way for Kagiso Malinga, while City threw on Kermit Erasmus for Ayanda Patosi soon after.
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SuperSport looked to mount a comeback late in the second half but the likes of Bradley Grobler and Aubrey Modiba were denied by a combination of good defending and good goalkeeping from Peter Leeuwenburgh.
In the end, City were able to see out the latter stages to hold on for the 2-0 and secured their spot in the next round.
City: Leeuwenburgh, Mkhize, Cupido, Kewuti, Kwanda,Patosi, Rusike, Modise, Mokeke, Martin, Links.
Subs: Stephens, Seedat, Norodien, Dove, Mthembu, Ralani, Erasmus.
SuperSport: Williams, Nhlapo, Mutale, Khumalo, Bhasera, Furman, Letsholonyane, Mokoena, Modiba, Mnyamane, Grobler.
Subs: Pule, Kekana,Daniels, Mahlatsi, Ntshangase, Webber, Malinga.