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The loss has almost dashed the Malabarians' title hopes.
Mohammedan Sporting Club rallied to hold Sreenidi Deccan 1-1 in another match to stay top of the table.
Gokulam won 2-1 with goals from Alex Sanchez and Abhijith K.
Alex sanchez converted a penalty to draw level, while Lalliansanga Renthlei struck in the third minute of added time as Gokulam extended their winning streak to five games.
The Malabarians outplayed Rajasthan United 4-1.
Gokulam won 2-0 to move into third position with 23 points.
Gokulam Kerala men defeated Inter Kashi 4-2 in the I-League while the women's team edged Odisha FC 2-1 in IWL.
The match will be played at a revised date.
Both teams were already out of the semifinal race. Punjab finished third with two points, while Gokulam ended at the bottom with a lone point in the four-team group.
Chennaiyin FC won 2-0 while Gokulam have lost both the games they played in the Cup so far.
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