As a result, the Clever Boys moved up to 13th spot on the league standings, while the Buccaneers, who tasted defeat for the first time this season, remain third on the table.
Pirates coach Milutin Sredojevic made several changes to the starting line-up that faced Cape Town City in a PSL match which was played at the FNB Stadium on Tuesday night.
Thamsanqa Gabuza made his return to the match day squad and he started alongside Lyle Foster upfront as Bucs looked to record another win after defeating City 1-0 at home.
Wits coach Gavin Hunt, who was under pressure due to the team's poor form - having lost 3-0 to AmaZulu in midweek, handed Gerard Phiri Jr his debut, while Steven Pienaar was relegated to the bench.
The Clever Boys were searching for their first league win of the season and they got off to the best possible start as they grabbed an early goal - five minutes into the match.
The Bucs defence was exposed following a free-kick and Phiri pounced - firing past goalkeeper Wayne Sandilands from close range to make it 1-0 to Wits.
The visitors nearly responded with a goal at the other end when Thabo Qalinge pulled the trigger from a tight angle and his effort hit the crossbar with Wits keeper Moeneeb Josephs well beaten.
Sredojevic's men kept possession very well in the Wits half as they looked to unlock the defence with Musa Nyatama dictating terms in the middle of the park for Pirates.
However, Ben Motshwari, the Wits captain on the night, was the shield in front of the hosts' defence - cutting out passes to the Pirates strikers Gabuza and Foster.
But the Wits defence was breached on the stroke of half-time and Josephs made a good save to deny Thabo Matlaba - ensuring that the first half ended with Wits leading 1-0.
Thabiso Kutumela, who has been in top form in the Multichoice Diski Chalkenge (MDC) this season, was introduced by Sredojevic six minutes after the restart as visitors looked to restore parity.
But there was lack of creativity in the final third as Qalinge and Mpho Makola were tightly marked by the Clever Boys defence which was marshalled by Bongani Khumalo.
The visitors kept probing and a rare chance fell for Makola just inside the box, but his curling effort was pushed away by former Pirates shot-stopper Josephs, and the hosts cleared their lines.
The Clever Boys were in a defensive mode in the closing stages of the match as they defended in numbers, while Eleazar Rodgers remained up as the only Wits attacker in the Pirates half.
Pirates could not find the equalizing goal and ultimately, Wits ran out 1-0 winners following a relatively quiet second half - with the PSL champions recording their first league of the season.