Chiefs went into the match unbeaten run in six matches across the league, and made just one change in Philani Zulu for the injured Khama Billiat.
The home side looked to continue their good run of form in all competitions, with Hendrick Ekstein flashing wide of goal after getting goal-side on 10 minutes.
With chances on both sides spare, Philani Zulu misfired from close-range on 22 minutes after being set up by Bernard Parker as the Amakhosi pushed for the breakthrough.
Injury though spoiled the Amakhosi’s intention, with Teenage Hadebe replaced by Ryan Moon on 37 minutes following a head injury.
The half ended in due course with little goal-mouth action to shout about on either end of the spectrum.
Moon missed a glorious chance on 52 minutes as he failed to find the target after rounding Elvis Chipezeze.
With virtually their first attack, Baroka went in front on 66 minutes as Tshidiso Patjie’s scorching free-kick from outside the area beat Bruce Bvuma hands down.
Ernst Middendorp installed their first change after realising what’s just unfolded, with Dumisani Zuma pulled on for Zulu a minute later.
Bakgaga dropped back, as Ekstein moved through the area to get a shot away which Chipezeze gathered comfortably.
Chiefs pressed for an equaliser in the final minutes, but the visitors held their ground to grab the maximum points and move off the bottom two spots with the hosts stuck in seventh.
Chiefs: Bvuma, Moleko, Cardoso, Hadebe, Ntiya-Ntiya, Mphahlele, Zulu, Maluleka, Adrianarimanana, Ekstein, Parker.
Subs: Akpeyi, Katsande, Booysen, Gordinho, Moon, Zuma, Frosler.
Baroka: Chipezeze, Ntswane, Mabeba, Sibiya, Gerbhardt, Mosele, Chinyenkentere, Makgaka, Semenya, Makgantai, Patjie.
Subs: Dlamini, Madubanya, Chivaviro, Ntshumayelo, Mongae, Makume, Mdantsane.