The victory sees Matsatsantsa remain fifth on the PSL log standings, while the Clever Boys slip down to third on the table.
Wits coach Gavin Hunt fielded a strong starting line-up with Frank Mhango leading the attack, while Bongani Khumalo filled the void left by captain Thulani Hlatshwayo at the back.
SuperSport assistant Kaitano Tembo, who was in charge of the team in the absence of Stuart Baxter, also named a strong side with Jeremy Brockie starting upfront alongside Thabo Mnyamane.
The Clever Boys and Matsatsantsa were both solid at the back in the opening stages of the league encounter and as a result there were no clear-cut chances created.
The home side enjoyed more possession with Phumlani Ntshangase and Thabang Monare controlling the midfield as they looked to feed the Wits attackers Mhango and Eleazar Rodgers.
Malawi international Mhango had a chance to put his side into the lead on the stroke of half-time, but SuperSport goalkeeper Ronwen Williams produced a good save to deny him.
The two sides were locked at 0-0 during the half-time break. This was because Wits and SuperSport were both cautious for most of the time in the first half.
A lively second half followed and Matsatsantsa looked like a rejuvenated side with SuperSport forwards Brockie and Thuso Phala keeping the Clever Boys defence busy.
Wits head coach Gavin Hunt responded by pulling out Mhango, who was tightly marked by the SuperSport defence most of the time on the night, and he introduced Phakamani Mahlambi.
But SuperSport continued to apply pressure on the Wits defence and in the 67th minute, Mnyamane found Phala, who fired past Wits goalkeeper Moeneeb Josephs to make it 1-0 to the visitors.
The Clever Boys relied on Mahlambi's speed and trickery in the remaining minutes of the encounter, but the new South Africa senior international's finishing was poor.
SuperSport had chances to extend their lead in the closing stages of the encounter, but they could not convert them and ultimately, they ran out 1-0 winners over Wits on the night.