Nhlanhla Vilakazi and Goodman Dlamini netted on either side of half-time as Ea Lla Koto secured their passage to the next round of the competition.
The Lions of the North had a brilliant chance to grab an early lead in the seventh minute, when Brandon Theron broke through one-on-one with Thela Ngobeni, but the midfielder was made to rue his decision to try and pass instead of shooting.
Mohammed Anas then had a clear cut chance just before the half-hour mark but Marlon Heugh pulled off a fine save to deny the Ghanaian striker.
Vilakazi then opened the scoring on the stroke of half-time as a lapse of concentration proved costly for Highlands.
Dlamini then doubled the home side's lead tapping in from close range in the 77th minute, handing Stars all but a place in the last 16.