Mohun Bagan, who had beaten Churchill Brothers 1-0 in their opening match in Barasat, now have six points from two matches to go past Aizawl FC at the top of the standings.
Embracing their home ground Rabindra Sarobar after winning a legal battle, the 2015 champions got off to some hits and misses before Duffy broke the deadlock with a 21st minute strike.
The Scot collected a brilliant cross and swerved past defenders and Shillong goalkeeper Vishal Kaith before firing it in with a clinical left-footer.
Their last match hero, Balwant kept the ball inside the box dodging Lajong captain Dan Gelu Ignat as Duffy lurking inside slotted it home with an angle.
For the Northeast outfit, who were hammered 0-3 by defending champions Bengaluru FC, this was their second successive defeat in as many games as they are yet to open their account.
Having won a legal battle, Mohun Bagan were allowed to play at their home venue by the National Green Tribunal yesterday.
The Mariners captain after a duel with Nimdorjee Tamang almost found the far corner with a grounded shot but the ball went a few inches wide in what was their biggest miss after the start.
After the break, Shouvik Ghosh triggered the through ball to Duffy and he ran in from the right to only hit it straight to Nimdorjee Tamang in a poor finish.
Shillong also dominated the proceedings after conceding the lead and looked for openings but failed to finish. In the 30th minute Chinglensana Singh struck a great free header but it went just over the goal post.
In the 56th minute, Zodingliana sent the ball towards the far end from a freekick but Mohun Bagan wall thwarted any further danger.
Sanjoy Sen brought in the AIFF 'Player of the Year' Jeje Lalpekhlua in the last few minutes and had a shot at the goal in the 2nd minute of stoppage time that went over.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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