The match went down the wire with Aizawl FC showing a lot of resolve as both teams were locked 1-1 at halftime after Duffy's second minute strike was cancelled by Jayesh Rane (41st) of the visiting side.
With 20 minutes left, the I-League debutants from Mizoram once again made their intention clear when Jeje Lalpekhula's 63rd minute strike was nullified by Ashutosh Mehta's header.
Amid intense drama, Mehta however failed to become their hero as he brought down Katsumi Yusa inside the box and Alfred Jayran saw yellow for his misconduct of kicking the ball out in what turned out to be a decisive 83rd minute for Mohun Bagan.
With five minutes of added time, Aizawl FC tried with all their might to bring it on level for a third time in the match but Mohun Bagan defence held up to remain unbeaten after six matches.
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Mohun Bagan are now have the same number of wins (five each) and draws (one each) as their bitter foes but behind them on goal difference.
The brace saw Duffy go past CK Vineeth to become the leading goal scorer with six goals from five matches.
Sehnaj Singh's through was intercepted but Katsumi Yusa took the possession and surged into the left wing as his cross was superbly headed home by the Scot with Aizawl defender Kingsley Eze failing to clear the ball.
Mohun Bagan could have easily doubled their lead through Prabir Das who slammed the ball into orbit but only to miss an open net.
Both teams fought hard and Aizawl kept pushing the game towards their wing every now and then to keep Mohun Bagan defenders on toes.
Finally Aizawl found the equaliser with five minutes to go for the break in what was a fantastic team effort. Lalmuankima began the move with an elegant through ball as Ivorian recruit Kamo Stephane Bayi cut inside the box with a grounded square pass before Rane found the goal with a first touch.
In the 63rd minute Jeje Lalpekhula scored against his home state with a calm left-footed finish from a clinical square pass from Prabir Das to put Mohun Bagan ahead again.
Mehta equalised in the 70th minute off Rane corner kick with a simple jump and heading the ball home without much fuss.
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