Jean-Michael Joachim scored early on while Ansumana Kromah equalised from the spot past the half-hour mark. The ten-men Chennai City then scored in the 71st minute through defender Veniamin Shumeiko to pick three crucial points for the visitors.
Sanjoy Sen made three changes to his starting lineup from the last game as Kinshuk Debnath and Nikhil Kadam were relegated to the bench. Raynier Fernandes was left out of the 18-man-squad. Rana Gharami and Azharuddin Mallick were summoned in. Young central midfielder Sourav Das was also given a chance.
Returning to action after 10 days, Chennai City FC dropped Alexander Jesuraj with Charles Lourdusamy shifting to the right flank. Sebastian Thangmuansang was replaced by Tarif Akhand at right-back and Murilo Almeida slotted alongside Jean-Micheal Joachim upfront.
The first dagger into the Green and Maroons' heart was punched in by Frenchman Joachim in the fifth minute itself. Sourav Das was embarrassed by Murilo who snatched the ball from him in the centre of the park.
The Timor-Leste national then trodded forward beating Rana Gharami and Eze Kingsley to release Joachim on the run and with only the keeper to beat, the former AS Nancy man beat Shilton Paul by targeting the top-left side of the net.
While the visitors continued to press hard, testing Shilton Paul a couple of times, the hosts remained toothless in attack. The first noteworthy attempt by the Mariners was in the 27th minute when Abhishek Das' cross was delivered to Ansumana Kromah inside the box but the Liberian hit the crossbar.
Surchandra Singh was brought in for Sourav Das who looked uneasy on his first I-League start. The former DSK Shivajians man sent in a free-kick which resulted in a goal-line save from Pradeep Mohanraj with Azharuddin Mallick' header on course to hit the net.
Mohanraj then turned villain for his team moments later, gifting Mohun Bagan their third penalty in four games. Ricky Lallawmawma's flag-kick was headed towards goal by Shilton D'Silva but Mohanraj blocked the ball from going straight into the net using his hand, thus getting his marching orders from referee Santhosh Kumar.
Ansumana Kromah made no mistake from the spot as the home crowd breathed a sigh of relief with ten minutes of regulation time in the first half still remaining. For the last three minutes including injury time, both sides were reduced to ten men when Shilton D'SIlva was taken off the pitch for a cut on his forehead he sustained from a ball which slammed on his face.
Even at the start of the second half, it was Chennai City who had put the foot on the gas with the Mohun Bagan attackers looking abysmal.
The referee had to issue two yellow cards to Edwin Vanspaul and Soosairaj at the same time in the 61st minute as the former brought down Faiaz and the latter slammed the ball right into Das' face.
Murilo won a corner all by himself and the ensuing flag-kick was delivered perfectly by Soosairaj as the Kyrgyz Republic-born Veniamin Shumeiko rose tallest to head in.
Murilo could have added in a third for his side in the 88th minute when his powerful shot only hit the bar.
It will be interesting to see if Mohun Bagan, who are now seven points behind league leaders East Bengal, will have a new person in-charge of the team when they next face Aizawl FC on Sunday.