The visitors went ahead in the 13th minute through Salulani Phiri's strike from the edge of the 18-yard box.
Ubuntu carved their first opening in the 23rd minute when Kamohelo Mahlatsi picked out Franklin Cale, who sent his effort inches wide.
Minutes later, the host went close again with Kanyiso Mayo skewing his close-range effort wide of the mark.
Ubuntu were rewarded for their perseverance just before the break courtesy of a goal from Ranga Chivaviro, 1-1.
Chivaviro was at it again three minutes into the second half by heading home from close range to put Ubuntu 2-1 up.
Rise and Shine's attempt at a comeback took a dent on 60 minutes when Sibusiso Mbonani was sent off for picking up his second yellow card.
However, Polokwane restored parity eight minutes later when Walter Musona fired past Khoza, 2-2.
Both sides pushed for a winning goal in the remaining stages of the half, but they were unable to carve out another opening, forcing the clash into extra-time.
The home side eventually restored their lead after 114 minutes when Siyambonga Madikane poked the ball home from close range.
That proved to be the final piece of action in the contest as Ubuntu held on to claim a memorable victory.
Ubuntu: Khoza, Sigwebela, Heutchou-Kullong, Fleurs, Bezuidenhout, Chiwunga, Adonis, Mayo, Chivaviro, Mahlatsi, Cale.
Subs: Gwala, Jacobs, Madikane, Sefoli, Sibanda, Isaacs, Goss.
Polokwane: Ndlovu; Tshehla; Hlongwane; Ravhuhali; Mbonani; Phiri; Vilakazi; Mngomezulu; Tlolane; Sulumba; Booi.
Subs: Semenya; W. Maluleke; Sikhosana; Musona; Chungwa; J. Maluleke.