The Clever Boys had a chance to open the scoring after 13 minutes though Gabadinho Mhango, who failed to hit the target from close range.
Four minutes later, Stars broke the deadlock courtesy of a header from Robert Ng'ambi from a corner.
Wits looked to hit back and they went agonisingly close in the 31st minute when Thabang Monare hit the upright.
The home side continued to throw numbers forward in search of an equaliser, while Stars were content to sit back and soak up the pressure.
Gavin Hunt looked to switch things up in the second half as Amr Gamal and Gerald Phiri were introduced.
The hosts did close got levelling matters three minutes into the half as Thulani Hlatshwayo headed wide from close range.
Eleazar Rodgers had a chance to put Wits level with 12 minutes remaining, but his header sailed wide of the target.
The Clever Boys threw everything forward in an attempt bag an equaliser but Stars managed to hold out until the final whistle.