Battling relegation, the defending champions exploited Mohun Bagan's fragile defence as an unmarked Balwant put the team ahead with a header in the 36th minute from a Thangjam Singh cross in the right.
A minute later, Churchill midfielder Alesh Sawant, while trying to clear the ball for a corner, scored an own goal to gift Mohun Bagan an easy equaliser.
Mohun Bagan went ahead in the 56th minute thanks to some inexperience goalkeeping by Lalit Thapa who brought down Christopher Chizoba inside the box for a resultant spotkick that was well executed by the Nigerian.
Bagan now have 19 points from 17 ties, while Churchill are 15 from as many matches to remain in the bottom half.
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The green and maroon brigade wasted opportunities in plenty especially after Churchill defender Dharmaraj Ravanan was brought down by their own goalkeeper Thapa in yet another shoddy display.
After the collision Ravanan suffered a head injury and had to be taken off on a stretcher with Churchill at the mercy of a weak defence but Bagan failed to bring in any field goal.
Coming in place of Ram Malik, Ujjal Howladar set up Sabeeth with a brilliant cross but the latter's shot found the inside of the post before rolling out just near the goalline.
Bencherifa brought in Shouvik Ghosh in the defence in the last minute but still could not plug the loopholes.
Balwant beat Rowilson Rodrigues by speed while the substitute was out of place before slotting home a gem from the
top of the box in the left to bring on the equaliser.