Rise and Shine came into the match full of confidence after holding Kaizer Chiefs to a goalless draw last time out and knowing a win would go a long way to securing their place in the top eight of the Premiership.
Stellenbosch started the match just outside the top eight in ninth and have been struggling for consistency this season, having won just eight of 25 Premiership games before the Polokwane encounter.
The two sides were evenly matched, though, and the first half was played at a breathtaking speed, with both teams creating chances.
Thabang Matuludi went close in the 15th minute when he sent a header just outside the post and Wonderboy Makhubu was denied by a fine save from Lindokuhle Mathebula seconds later.
Polokwane were the better of the two sides after the break and it seemed just a matter of time before they would find the back of the net. Bonginkosi Dlamini had a shot brilliantly saved by Sage Stephens around the hour mark.
Just when it appeared as if it wasn't going to be Rise and Shines day, Manuel Kambala struck a minute into stoppage time at the end of the game with a close-range effort to grab the points, moving his side up to sixth in the standings.
Elsewhere in the Premiership on Sunday, Bernard Parker's first game in charge of TS Galaxy ended in a 0-0 draw against Magesi FC at Mbombela Stadium.
The Rockets made three changes to the side that lost to Richards Bay in mid-week and they struggled early on against an in-form Magesi side, who came into the match off the back of a win against Durban City.
The biggest chance of the first half fell to Sifiso Luthuli, who got played in behind the Galaxy defence but was denied by a fine save from Ira Eliezer Tape.
The Rockets looked much improved after the break and dominated the first 10 minutes after the restart but struggled to create meaningful chances.
Soon Magesi were able to take hold of the game again and Thabang Sibanyoni went within inches of giving them the lead but his headed effort went just wide.
In the end, neither side was able to find a breakthrough and they had to settle for a share of the points.
Mamelodi Sundowns moved back to the top of the Betway Premiership after grinding out a hard-fought 1-0 victory over Polokwane City at Seshego Stadium on Wednesday night, edging ahead of Orlando Pirates in the title race.
TS Galaxy striker Junior Zindoga says the players must take responsibility for the sacking of head coach Adnan Beganovic.
Polokwane City head coach Phuti Mohafe is confident of a result against Mamelodi Sundowns in the Betway Premiership on Wednesday.
TS Galaxy interim head coach Bernard Parker is determined to lead his team to a historic second Nedbank Cup final victory.
