Chinglensana Singh (33rd minute) and Fabio Pena (62nd) scored for Lajong minute while Do Donghyun found the target for East Bengal in the 44th minute.
Lajong, who had beaten East Bengal last Sunday in their final I-League match here, now have an advantage before their away game against the same opponents on May 4.
Englishman Trevor Morgan thus began his second stint as East Bengal coach with a loss. Morgan, who coached East Bengal from 2010-13, succeeded Biswajit Bhattacharya who had resigned following their poor form in the I-League.
Lajong were a relaxed lot coming into the tie and the approach seemed to help their cause early on with the East Bengal back line feeling the heat.
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The first real opportunity came Lajong's way in the eighth minute following a Bipin Singh corner kick which Fabio Pena headed just wide. Three minutes later, Issac Chakchuak sent his lofted shot over the bar from just outside the box.
However, the joy of the local fans was shortlived as barely 11 minutes later Do Donghyun converted after being delivered with a fine ball by Ranti Martins.
Following a long ball forward from Lalrindika Ralte, Ranti caught it just before it went out and flicked it over for a charging Do Donghyun to head past Vishal Kaith for the equaliser as both side went into the break tied 1-1.
However, barely were the changes been made that Fabio Pena changed the fate of the game. It was after a series of passes from close range on the right between Issac and Bipin that the ball fell to Fabio who made no mistake in converting it. Fabio's tamed shot rolled into the nets as Rehenesh was caught unawares in the melee.
Signs of desperation were clearly visible in the East Bengal ranks thereafter as the match drew closer to full time. But a crowded Lajong backline meant that the visitors were unable to make any significant inroads.