Jacky Motshegwa hit a brace for the NFD leaders to go with a goal from Loyiso Simandla, while Andile Mbenyane and Rhulani Manzini netted for the Chilli Boys at Buffalo City Stadium.
Motshegwa opened the scoring 27 minutes in, as his free-kick took a deflection and sailed into the far corner of the goal.
Simandla doubled the advantage three minutes later, poking into an empty net after doing well to evade Daniel Akpeyi's challenge.
Mbenyane pulled one back on the stroke of half-time with a cool finish past goalkeeper Veli Mothwa.
Motshegwa, however, got his second goal on the hour-mark after creating space for himself on the edge of the area.
Manzini then reduced the deficit three minutes later following a blunder by Mothwa.
Chippa pressed in the latter stages, but Lerato Chabangu and Thamsanqa Sangweni wasted chances from close range, while Dylan Goss had a header brilliantly foiled by Mothwa.
Chippa: Akpeyi, Macheke, Okwuosa, Cloete, Chipeta, Mlambo (D Goss 84'), Zuke (Sali 36'), Sangweni, Manzini, Mbenyane, Bance (Chabangu 62')
Baroka: Mothwa, Ntsoane, Nkabinde, Shaku, Rhavhuali, Mtshali (Mothupa 48'), Simandla, Motshegwa, Magaka (Letsoalo 69'), Mokondelela (Kutumela 80'), S Sangweni