The red and gold central defender headed in the winner from a Sanju Pradhan corner kick in the 83rd minute after both sides were locked 1-1 with goals on either side of the break.
Mohammad Rafique helped East Bengal scored the opening goal of the match in the 38th minute after being set up by Mehtab Hossain as he went past Brian Mascarenhas before putting the ball past a diving Karanjit Singh.
Darryl Duffy restored parity in the 65th minute after receiving a long ball from Augustin Fernandes to put pressure on the home team.
The Goans, on the other hand, remained eighth in the table with five points from eight matches.
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Salgaocar tried their best for another equaliser but apart from testing Luis Barreto with a header in the 90th minute, they weren't able to create any opportunities for a late second goal.
East Bengal looked better of the two sides but it was Martin Scott of Salgaocar who remained the home side's nemesis with his delightful moves.
Mendy then turned provider in the 22nd minute as he played in Mohammed Rafique but the Indian forward was unable to make use of the opportunity.
Rafique, however, made amend the next time to take East Bengal forward.