The win takes Churchill Brothers to 12th place above Mohammedan Sporting with 18 points while Pune FC's chances for the title diminished as they remained on 30 points from 19 matches and are placed third.
Churchill Brothers who needed a win to move above Mohammedan Sporting got a rude shock early in the match when they were down to 10 men after Satish Singh got marching order from referee Pratap Singh for a foul in the 13th minute.
Jaison Valles made a run on the left flank while Salam Ranjan Singh put up a sliding tackle. The ball landed in the path of Anthony Wolfe who found the back of the net to put Churchill into the lead.
Pune FC too were reduced to ten men latter in the first half when keeper Aminder Singh who left his charge and tried to sweep the ball off the feet of Wolfe but caught the foot of Wolfe and referee gave him marching order.
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With both the teams playing with 10 men after the change of ends, Churchill Brothers had clear chance to forge ahead but Arup Debnath who replaced Aminder Singh brought off good saves when he blocked Leny Rodrigues shot in a one-0n-0ne situation.
Pune FC made a counter move and Pierre rattled their rival woodwork with a pile driver.
Pavlovic who had his hand in the equaliser in the first half than put Pune FC in the lead in the 69th minute after being set up Anthony D'Souza. He was fed by Gabriel Fernandes.
Balwant Singh who has been their saviour in defeat found the equaliser in the 90th minute when he strolled past the rival defence and put the ball at the back of the net.
With five minutes added time, Binesh Balan than gave Churchill Brothers victory as he slotted the ball home in the fourth minute of the injury time after Lenny Rodrigues cross to Wolfe who headed the ball back to Balan to finish off the move.