Goals from Edgar Manaka and Carlington Nyadombo sealed Rise and Shine’s passage into the quarterfinals for the first time in their history – victory also their first in Rustenburg in four attempts.
Robert Ng'ambi opened the scoring on the day, while Gift Sithole received his marching orders in second-half stoppage time.
Ng’ambi opened the scoring on 11 minutes, having capitalised on a poor clearance from a free-kick, and Muzikayifani Ngidi could only succeed in deflecting his diving header past George Chigova.
After Ndumiso Mabena, fresh off Bafana Bafana duty, guided his shot narrowly wide, Manaka popped up to level matters in first-half stoppage time with an expert header from a Themba Mavundla cross.
Both teams hit the woodwork in the second stanza. Sphesihle Nzimande went close for the hosts before Kobamelo Kodisang was unlucky to see his shot hit the underside of the crossbar.
Polokwane were the better side heading into extra-time – this despite Julio Leal fielding a second-string side – and their task was made easier after Sithole saw red.
Ryan de Jongh was brought in to fill the gap left by Sithole, but he could only succeed in giving away the penalty that lead to the winning goal; Nyadombo with a cool finish to seal Polokwane City's progression in the tournament.