Mahmood Al Ajmi (77') and Henry Kisseka (90') found their names on the score-sheet for the visitors while Aser Dipanda Dicka (78') netted the consolation goal for the home side.
Shilton Paul retained his place under the sticks and had Kingsley Eze and Rana Gharami in front to marshall the defence. Cameron Watson and Raynier Fernandes had the keys to midfield whereas Aser Dicka partnered Lebanese striker Akram Moghrabi upfront.
On the other hand, Bino George decided to make four changes for Gokulam Kerala as Balwinder Singh, M.D Dibin, Arjun Jayaraj and Laldampuia got replaced by Provat Lakra, Daniel Addo, Mohammad Rashid and Kivi Zhimomi.
Kerala took the game by the scruff of its neck making their intentions known from the very first minute. The first real chance also fell for the visitors when Henry Kisseka's narrow-angle effort was denied by the woodwork before he showed a clean pair of heels to Bagan right back Arijit Bagui.
Mohun Bagan took some time to settle into the game before they started making in-roads into Kerala's defence.
Just over the half-hour mark, Arijit and Faiaz combined well to supply a good ball towards Watson in the middle. The Australian laid it off for Nikhil Kadam, whose shot was not cleanly collected by Bilal Khan on the first attempt. Dicka tried to score from the fumble but the goalie eventually recovered.
Although Mohun Bagan had upped the tempo after the initial moments of the first half the Maroon and Green brigade could not find the opener, as both teams headed towards the tunnel with a 0-0 scoreline.
Bagan continued to pile pressure on Kerala's defence but the lack of quality in the attacking third was letting Sankarlal Chakraborty down.
Akram's 63rd-minute miss from three yards out will be one of the contenders for the miss of the season. Arijit put in an inch-perfect cross for Akram whose feeble tap-in was blocked by Bilal. The woodwork also helped the goal-keeper as the ball did not trickle in after the initial block.
The Mariners got punished in the 77th minute for some sloppy defending at the back when Mahmood Al Ajmi performed the role of a poacher par excellence after Henry threaded in a perfect ball for him on his right foot.
Bagan responded instantly with an equalizer when Dicka scored his ninth goal of the season as substitute Bimal Magar served him with a ball on the platter from inside the six-yard box onto his head.
When Henry's thumping volley found the back of the net just at the stroke of the 90th minute complete silence enshrouded the entire Saltlake Stadium. Musa controlled the ball well before whipping it into the way of Kisseka whose venomous volley left Shilton Paul rooted to the ground as the ball flew past him.
Mohun Bagan threw in all their attacking resources in the last seven minutes of injury time but the woodwork once again denied them a goal which would have ensured at least a point for the home side.