Wits made a bright start when Simon Murray turned inside the box to smash home a loose ball after 38 seconds played.
Stars were on the back-foot and a run from deep by Cole Alexander nearly led to a second but good goalkeeping from Badra Ali Sangare kept him out on five minutes.
Murray was invited to grab his brace but after good touches on the ball, send the close-range shot narrowly wide.
Ea Lla Koto tried to launch a way back, but weren’t able to penetrate the defensive block from the Students with most of their passes going astray.
At the midway stage, Deon Hotto fired horribly over the top after being set-up by Murray leaving coach Gavin Hunt fuming on the touchline.
Darren Keet made his first save for Wits with Sthembiso Dlamini’s running header following a corner kick on the half and hour mark.
In the second half, Wits dominance didn’t subside with pressure aplenty on the home side. The instigating passes from Alexander did on occasion find his teammates but not in good areas.
The Bethlehem side began growing in confidence and Dlamini was denied by the left-hand post after turning from a metre inside the box on 54 minutes.
Stars introduced their first change when Judas Moseamedi replaced Linda Bhengu after 56 minutes played.
Wits responded with their first change and brought on veteran Elias Pelembe for Haashim Domingo four minutes later.
With a quarter-hour remaining, Moseamedi brought down a ball from the left but failed to find the target with a horrid execution that flew over the bar to the dismay of the supporters.
Former Kaizer Chiefs and Orlando Pirates striker Lehlohonolo Majoro was brought on to try and seal the contest in an immediate swap with Murray.
Moseamedi threatened again after 79 minutes when making space for himself, unleashed a thunderbolt that cracked the frame of the woodwork.
The defending champions survived the late flurry from the hosts to book a spot in the last eight, on course to defend their title.
Stars: Sangare, Mahamutsa, Phungwayo, Tema, Dlamini, Maruping, Makhaula, Jantjie, Bhengu, Mobbie, Tchilimbou.
Subs: Kwizera, Keita, Mbhele, Masina, Gandze, Rodgers, Moseamedi.
Wits: Keet, Hlatshwayo, Nonyane, Johannes, Monare, Murray, Hotto, Mkhwanazi, Alexander, Domingo, Macuphu
Subs: Mhlongo, Mere, Pelembe, Motupa, Ritchie, Dzvukamanja, Majoro