Veteran Malawian Esau Kanyenda was the hero for the strugglers with both goals, while Aces' response came through Abia Nale.
It was a poor first half as both teams struggled to find any sort of rhythm, but Kanyenda got the opener in the 14th minute, capitalizing on some poor defence before toe-poking past Bafana Nhalpo.
Aces had a chance through Tendai Ndoro which was saved, but Nhlapo had to be at his best again just before the break after another defensive mix-up.
The second 45 was a much better affair and saw Aces quickly draw level thanks to a goal from Nale five minutes after the restart, having been played in by Mabhuti Khenyeza.
Eight minutes later Polokwane were afforded the chance to take the lead for the second time when Bafana Nhlapo pulled down Kanyenda inside the box and the referee awarded a penalty.
Vukile Mngqibisa stepped up for Polokwane, but failed to convert from the spot as Nhlapo produced a fine save.
However, just four minutes later and Polokwane did take the lead when Kanyenda grabbed his second of the afternoon with an expert finish after latching onto a through-ball from Kabelo Lichaba.
Aces tried to get back into the match after that, but were unable to break down the Polokwane defence as they held on for all three points.
The result sees Boebie Solomons’ side up to 14th place with 27 points from 28 League games, three points ahead of the relegation zone, while the loss for Aces sees them remain in sixth place on the table.