The victory saw Bakgaga Ba Mphahlele advance to the Last 16, while Rise and Shine bowed out of the tournament.
Rise and Shine started the match brightly and they threatened first through their long-serving attacker Puleng Tlolane a few minutes into the game.
Tlolane unleashed a curling effort from range and Baroka goalkeeper Elvis Chipezeze produced a fine save to deny the hosts the opening goal.
The home side should have broken the deadlock through Mohammed Anas after Bakgaga Ba Mphahlele had failed to clear a cross from the right.
However, the Ghanaian centre forward hit the upright from close range with the Baroka defence exposed, while Chipezeze could only watch on.
Clinton Larsen’s men continued to create chances with the halftime break approaching, but they were very wasteful in the first-half.
Anas had an opportunity to score from inside the box and he placed his effort wide of the target and the two teams were locked at 0-0 at the interval.
Baroka came back an improved side following their halftime team talk with coach Dylan Kerr.
The English tactician introduced former Bidvest Wits and Ajax Cape Town striker Prince Nxumalo as the visitors looked to break the deadlock.
Nxumalo proved to be a super-sub as he scored from Gerald Phiri Jr’s corner-kick to make 1-0 to Baroka with 16 minutes left on the clock.
Larsen reacted by introducing Jabulani Maluleke and Sibusiso Hlubi with Polokwane looking to grab a late goal and take the match into extra-time.
However, the visitors were solid at the back in the closing stages of the match and ultimately, Baroka emerged 1-0 winners over Polokwane.