Prince Nxumalo came off the bench to scramble the goal home from a Gerald Phiri Jr corner kick in the 73rd minute.
City who were the hosts of this Limpopo derby started the match showing intention to score but Puleng Tlolane, Mohammed Anas and Walter Musona could only come close.
The winning coach Dylan Kerr says his side got what they deserved from the encounter.
Bakgaga will play ABC Motsepe league side Hungry Lions in the last 16 round. Meanwhile, Kerr adds that the wet conditions on the night made it difficult for his charges to play how they wanted.
However, Kerr says he is proud of his players for digging deep especially the frontline and the defense which saw Denwin Farmer win Man of the Match.
The losing coach Clinton Larsen was upset at the result saying it is the same old story with his charges where they create but don’t bury their chances.
Larsen handed defender Dennis Chembezi a debut and also gave Eden Nene his first start this year as well.
The coach feels the debutant struggled in the beginning but found his feet as the game progressed adding that Sicelokuhle Hlatshwayo also performed well. Larsen admits that it has been difficult getting consistency in defense selection wise due to injuries. – Report by Lethabo Kganyago