The Ugandan earlier set up Mahmood Al-Ajmi's peach of a goal in the 77th minute before Mohun Bagan took less than a minute to restore parity through season's leading scorer Dipanda Dicka who brought up his ninth goal with a calm and composed header.
Just when it was meandering towards a draw, a world-class volley by Henry gave Mohun Bagan the heartbreak as the 2015 champions signed off their campaign at home with a shock defeat that will continue to haunt forever.
The win lifted Gokulam from the bottom, going past Chennai City on better head-to-head count as the Kerala outfit secured their fourth win from 13 matches, of which three have come in away matches.
Mohun Bagan needed more accuracy in their passes and finishing as their sloppy display was a big let down for the Shankarlal Chakraborty coached side.
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The Kerala outfit made the best use of their chances.
Akram Moghrabi could not have asked for a better supply, as Arijit set it up from the right with a low cross as there was no one from Kerala defence to stop it.
But a weak Akram strike found goalkeeper Bilal Khan on his path and the Lebanese also failed to strike from the deflection, with his shot hitting the woodwork.
Minutes later, Akram's stint on the pitch was over and was replaced by the Nepalese import Bimal Magar.
Henry, who brilliantly controlled the long ball, threaded the two defenders to give it to Alajmi in the box who shot it past Shilton Paul.
It did not take very long for Mohun Bagan to respond as Dicka found his ninth goal with a fantastic header supplied for him by Magar.
Dicka in the meantime was adjudged man-of-the-match but as it turned out it was Henry who turned out to be the real hero with his stunning goal in the 90th minute.
To add salt to their injury, Mohun Bagan were denied by the woodwork when Dicka's powerful shot ricocheted off the bar.
In the 34th minute, S K Faiaz was brought down by Provat Lakra inside the box but the referee thought otherwise, bringing displeasure to the home camp.