Lehlohonolo Majoro almost opened the scoring in the sixth minute with a header inside the box following a good cross from Sifiso Myeni, but he could not keep his header down and on target.
Gavin Hunt's charges dominated after 15 minutes, playing high up the pitch while Stars were defending in numbers.
Daylon Claasen could have given the home side the lead in the 29th minute with a low shot inside the area but Badra Ali Sangare made a brilliant reflex save.
Three minutes later, Thamsanqa Teyise sensationally grabbed the lead for Luc Eymael's troops with a volley that found the back of the net following a corner, 0-1.
Majoro had a chance to equalise in the 40th minute with a volley following a cross from Claasen but he could not find the target.
The first half ended with Stars having the 1-0 lead despite the Clever Boys dominating play.
The hosts came out firing in the second half playing with more intensity ten minutes into the second stanza.
Majoro should have equalised on the hour-mark after being picked out by Daine Klate, but somehow could not find the target after going through on goal at the far post.
Klate was withdrawn in the 69th minute and was replaced by Vincent Pule as Hunt looked to turn things around upfront.
Pule had a crack at the goals from just outside the box with 15 minutes left to play, but his strike well collected by Sangare.
Edward Manqele was introduced with five minutes left to play in place of Mohammed Anas for Stars, while Gabadinho Mhango replaced Myeni for the hosts.
Eymael's troops stood resolute at the back and were well organised to claim the 1-0 win over struggling defending champions.