Chippa showed the early promise with a free-kick from Mark Mayambela near the edge of the box, but it sailed over the top.
The home side responded in the way they always do, with numerous attacks on goal, but struggled to break down the defence that held their lines very well.
It didn’t stop the likes of Siphelele Mthembu, Sthembiso Dlamini and Harris Tchilimbou from continuing their harassment, but they were unable to beat Brighton Mhlongo.
Pressure on the other side continued, with Thabo Rakhale calling Thela Ngobeni to outstanding reflexes nine minutes to halftime.
Ea Lla Koto wasted no time going ahead, with an instant strike by Paulus Masehe from a set-piece at the start of the second half.
Chippa responded with a similar scenario, with Linda Mntambo finishing off a free-kick following a foul on Algerian-born Fares Hachi in the 57th minute.
Mohamed Anas, who scored a late brace last Saturday, looked to restore the lead but failed to test Mhlongo a minute later.
New coach Vladislav Heric made his first change, bringing off Mxolis Machupu for former Stars striker Edward Manqele in the 63rd minute.
It was followed with the arrival of Bantu Mzwakali for the lively Mark Mayambela five minutes later in a lukewarm Bethlehem city.
Manqele made hard work of a perfect opportunity inside the box when he blasted the effort over the bar with the ball falling kindly for him minutes from coming on.
The hosts was also caught in this particularly guilt with Mzwakali misfiring from close range with the goal at his mercy.
Bengali Keita propped up inside to hand Stars the lead once again and steer them to the quarterfinals where they join Ubuntu Cape Town and Baroka FC.
Stars: Ngobeni, Masehe, Mobbie, Mahamutsa, Keita, Phungwayo, Anas, Tchilimbou (Teyise 89’), Dlamini (Makhaula 71’), Jantjie, Cosse (Mthembu 65’).
Subs: Sangare, Makhaula, Vilakazi, Mthembu, Mashego, Teyise, Klaas.
Chippa: Mhlongo, Macheke, Okwuosa, Nsabiyumva, Lentjies (Mntambo 46’), Rakhale, Hachi, Mabaso, Mayambela (Mzwakali 68’), Sali, Macuphu (Manqele 63’).
Subs: Akpeyi, Mdlinzo, Seanego, Mzwakali, Bergman, Mntambo, Manqele.