Chiefs broke the deadlock after eight minutes as George Maluleka collected a pass from Bhongolethu Jayiya, before rifling the ball into the top corner from 25-yards out.
Baroka did not sit back as they pushed for an immediate equaliser with Richard Matloga causing havoc down the right, although none of his teammates could convert his crosses in the opening 15 minutes.
The visitors were eventually rewarded in the 22nd minute when Lewis Macha got in front of Erick Mathoho and sent a header past Itumeleng Khune.
Chiefs were then dealt a blow after 37 minutes when Gustavo Paez was forced off with an injury and replaced by Bernard Parker.
Both sides pushed for another goal in the remaining stages of the first half, but they were unable to carve out another clear-cut chance.
After a quiet start to the half, Baroka had a chance to take the lead in the 56th minute but Sipho Moeti volleyed from just inside the box.
Two minutes later, Baroka were in front as Gift Motupa created some space in the box, before unleashing a powerful effort that left Khune with no chance, 1-2.
Steve Komphela responded by introducing Dumisani Zuma for Jayiya on the hour mark, before William Twala was introduced on 77 minutes.
Chiefs were camped in the Baroka half for most of the second period, but were let down by their decision-making in the final third.
The hosts went close to levelling matters in the 86th minute, but Mathoho could only direct his header straight at Virgil Vries.
Chiefs pushed for an equaliser in the closing stages of the match, but they were unable to get another chance as Baroka held on for the win.