Makhehleni Makhaula, Mohamed Anas and Sinethemba Jantjie all scored for the home side, while Cuthbert Malajila grabbed a consolation goal for the Clever Boys.
But it is how they build on this solid performance that would put behind what has been a very disappointing and difficult season for them.
If Gavin Hunt had his way, Wits would not have travelled to Bethlehem given their terrible record against Stars.
Prior to this encounter, the Students had beaten Stars just once in the last nine matches in all competitions, and Hunt knew that they were in for another tough battle.
Wits were awful defensively, and they will look back and bemoan this performance should they fail to wrestle the title away from Sundowns in the remaining two matches.
The champions elect went into the break trailing Ea Lla Koto, thanks to Makhaula's 24th minute strike.
The visitors failed to convincingly clear their lines, and the ball fell perfectly for the Stars midfielder, who pulled the trigger from the edge of the box to make it 1-0.
The Clever Boys lacked venom and hardly threatened a stubborn Stars defence marshalled by Rooi Mahamuts and Thamsanqa Teyise.
Hunt's charges looked very promising in the early stages of the second half, but put the foot off the gas in after the hour-mark. Sifiso Mbhele dispossessed Phumlani Ntshangase outside the box, before firing towards goal. His shot came off the woodwork with Moeneeb Josephs well beaten, but Anas was in the right place at the right time to slot the ball into an empty net.
The small crowd at Goble Park got behind the home team, making it difficult for Wits players to concentrate on the game even after the changes Hunt made midway through the second half.
However, things got tense when Wits pulled one back through Malajila with 16 minutes left on the clock, but Stars didn't panic as they maintained discipline at the back before killing off any hopes of a comeback with a late strike.
Thela Ngobeni's long ball upfront found Anas, who broke away on the counter, before setting up Jantjie to wrap seal a remarkable win for Stars.
Wits surely learned a thing or two from this game that if they really want to win the league, they will need to defend better and be ruthless in front of goal.