It was a successive meeting in the matter of weeks between the two sides after playing to a draw in a recent Absa Premiership clash.
After losing the MTN 8 recently, United hoped to grab the opportunity for a last eight berth and made a bright start from the get go.
Ghampa Lungu did well to press high in the first minute to draw a save from George Chigova, with Teboho Mokoena unable to bury the rebound.
Bafana Bafana international Aubrey Modiba missed another good chance for United from an acute angle, with Chigova punching clear at his near post.
Englishman James Keene rushed into the box and attempted a half-volley but weren’t able to beat Chigova just before the half and hour mark.
The pressure from United continued in the second half and Modiba found the side-netting after finding space out wide.
In a rare offensive foray, Vusumuzi Mngomezulu was denied by Ronwen Williams after trying to beat him with a shot from afar.
Brilliant defensive work from Onismor Bhasera then prevented City once again from surging in front with a half-chance from Rodney Ramagalela.
SuperSport made its first change as veteran Thuso Phala entered for Modiba on 72 minutes. With that, the deadlock was broken.
And it was the self-same Phala making no mistake to lob Chigova after holding off the defence inside 76 minutes.
It’s a lead the Tshwane giants held on to despite an immediate attempt from the hosts. Although Edgar Manaka denied the win in added time after home a corner to send the game to extra time.
Ten minutes into extra time, Clayton Daniels ballooned over the top and missed the opportunity to put them back in front from a good goal-scoring situation.
Grant Kekana responded later on with a similar effort only with his head, which he failed to make it count after heading wide instead.
The match was settled on penalties, and SuperSport made light work with successful conversions for a 6-5 win.
Polokwane: Ndlovu, Mvelase, Hlongwane, Nkili, Mbonani, Seabi , Mngomezulu, Manaka, Anas. Malulek, Booi.
Subs: Phali, Sikhosana, Miya, Musona, Tlolane, Baloyi, Phiri.
SuperSport: Williams, Daniels, Khumalo, Bhasera, Kekana, Ntshangase, Mokoena, Letsholonyane, Modiba, Lungu, Keene.
Subs: Pule, Boateng, Nhlapo, Gould, Phala, Mahlatse, Le Roux.