Having missed a flurry of chances, Mohun Bagan finally broke the deadlock in the 36th minute Pritam Kotal's goal bound cross dipped and beat the goalkeeper finding back of the net.
Sony Norde made amends for some costly misses when the Haitian recruit sealed the win with a swerving free-kick in the 63rd minute to ensure full points for the green and maroon brigade.
Their first win from four matches enabled Mohun Bagan to again go atop the table by virtue of better goal difference despite having logged same number of points with Bengaluru FC (35 each).
The goal came out of the blue for the green-and-maroon brigade, whose frontmen lacked finishing skills even as they held a greater share of the possession early on.
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Sony Norde, Jeje Lalpekhula and Balwant Singh all had at least two chances each but all went abegging.
The Haitian forward wasted two chances in two minutes in front of the net and in the 23rd minute Katsumi Yusa was brought down on top of the box.
Thankfully for Mohun Bagan, the Korean's strike landed straight to Shilton Paul. Nothing going their way, Mohun Bagan went ahead with Kotal angular powerful shot.
Mohun Bagan could have doubled their lead but Balwant and Jeje both had sloppy outings for the slender lead at the break.
The spirited debutants on the other hand looked threatening on the counter attack but luck swayed Mohun Bagan's favour with Shilton Paul coming in the way of the Shillong outfit.