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Emil Benny, Dennis Antwi, Lalromawia and Ronald Singh in the second half gave the Malabarians much-needed three points to go fourth with 13 points in eight matches.
Gokulam improved their tally to 10 points from seven matches with the win.
Twelve teams are in the fray.
Aizawal picked up up their first win this season to move up to fifth place.
Gokulam, who trailed 0-2 and 1-3, hit back with three goals in the space of six second-half minutes to ensure three points.
Gokulam outplayed BSS Sporting Club 7-2 to finish second behind United SC in Group D. They will take on Mohammedans in the quarterfinals.
Sarkar scored the winning penalty in the eighth minute. Mohammedans will take on Real Kashmir in the semifinals.
The Kerala-based side had been at the receiving ends twice in the last edition but they stole a vital point against the Manipuri outfit at the Khuman Lampak Stadium.
Gokulam will play their first I-League match on October 27 against Mohun Bagan at the EMS Stadium in Kozhikode.
Gokulam mounted a late fightback deep into the added time, when Joel Sunday scored twice in the last two minutes of injury time.
Results 11-20 of 71
