Goals from Katlego Pule and Bhongolwethu Jayiya at Royal Bafokeng Stadium broke a 14-match winless streak for the Clever Boys; their first three-pointer of 2012.
After the teams exchanged some early half-chances, Stars' Themba Ntumba almost scored a cracking long-range goal in the seventh minute, but Eduan Naude tipped the shot over his crossbar.
On 16 minutes it was Jackson Mabokgwane's turn to make a fine save, plucking Brad Phillips' shot from the edge of the penalty area out of the air.
Just two minutes later Mabokgwane was helpless to deny Pule, who opened the scoring from close range after some sloppy marking by the hosts.
Wits extended their lead on 21 minutes when Bhongo Jayiya fired home a shot from the edge of the box, finding the top left corner of the net with his right-footed effort.
Stars almost pulled a goal back six minutes later, with former Orlando Pirates striker Chiukepo Msowoya directing a header on target, but again Naude was equal to the task and made a good save.
Msowoya had another headed effort a few minutes before the half time break, but he was unable to direct it on target.
Stars used all three of their substitutions within the first 15 minutes of the second half, but it was Wits who looked the likelier scorers.
Wits almost added to their lead in the 53rd minute when Jayiya got a shot away from inside the penalty area, but Mabokgwane again came up trumps.
Stars dominated the last quarter of the game, but they found Naude a hard man to beat: he came up with a fine save on 81 minutes when he tipped Henrico Botes' goal-bound header over the bar.