Chencho, known as 'Bhutan's Ronaldo' scored in the 23rd and 30th minute as new chief coach Shankarlal Chakraborty's honeymoon period was over within his second match.
Kingsley Eze pulled one back for Bagan at the Salt Lake Stadium but that surely wasn't enough.
Minerva are now on top of the points tally with 19 from 8 matches while East Bengal are on 18 points having played 9 games.
Mohun Bagan's dreams of winning the league are slowly fading away as they are placed fifth with 13 points from 9 games.
Minerva Punjab, on the other hand, went for an extra man in defence as Deepak Devrani earned his place in the starting XI replacing goal-scorer of the previous match Gagandeep Bali.
The Mariners had three flag-kicks in the first ten minutes but failed to make them count.
It was the Bhutanese international Chencho who drew the first blood as he first dodged past the defender and fired a bullet-shot towards Shibinraj, who was completely taken by surprise.
Within minutes Minerva Punjab could have doubled their lead, but this time the goalie came out on top in a one-on-one situation with Chencho.
But the Punjab side did not have to wait long for their second goal as the Minerva number 7, produced a world-class finish at the far post after an inch-perfect through was threaded to him by William Asideu.
Mohun Bagan got the opportunity to peg one back on the 36th minute, but Ansumana Kromah failed to convert from the spot with a feeble attempt which was saved comfortably by Rakshit Dagar diving low to his left.
Mohun Bagan started the second half with the same tempo, but their reported efforts to breach Minervas defence were turning futile.
Just after the hour mark, Aser Dipanda pulled the trigger from point-blank range after Kromah played it to him, but his effort was directed straight towards Dagar who fisted away to safety.
Minerva continued to maintain shape and their defensive organisation remained a hard nut to crack.
Dipanda got another shot at the target during the injury time, but his effort went across the face of the goal without testing Dagar.
Mohun Bagan will go into the Kolkata derby on January 21 at the back of this defeat whereas Minerva Punjab will next face Shillong Lajong on January 14.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)