The Citizen started brightly with Ayanda Patosi threatening to create goal-scoring opportunities with his pace upfront.
However, Abafana Bes'thende settled in the game and controlled the midfield after 20 minutes to deny City the chance to supply their forwards.
Siphelele Magubane duly grabbed the lead for Clinton Larsen's charges in the 39th minute with in impressive finish past Sage Stephens.
Benni McCarthy's troops were showing the determination to come back into the game and Letsie Koapeng had a fantastic chance to bring them level two minutes before the break but he fluffed his chance inside the box after being gifted acres of space.
Ebrahim Seedat also had an opportunity to level the scores in first-half stoppage time, but his fierce strike sailed over the bar.
Sibusiso Masina almost equalised spectacularly for City in the 56th minute with a half-volley inside the box but his effort missed the target.
City were creating chance after chance going into the hour mark with the hosts under siege.
However, Larsen's troops extended their lead to 2-0 in the 69th minute through Jabulani Shongwe following a corner.
Ayanda Patosi pulled a goal back for the Mother City side in the 80th minute from the penalty spot, 2-1.
The match was open with end-to-end attacks after 85 minutes and City equalised a minute before time through Thabo Nodada to earn themselves a point after coming from two goals down.