Mohammed Rafique (44') scored the only goal of the game as the Red and Golds took advantage of Minerva Punjab FC's slip against Aizawl FC earlier in the day.
Khalid Jamil brought in Mohammed Rafique, sacrificing fullback Lalramchullova as Prakash Sarkar slotted in at right back. Charles De Souza kept his place alongside Willis Plaza up top as Katsumi Yusa started on the left flank with Laldanmawia Ralte shifting to the right.
Kamo Stephane Bayi was passed fit to start as Usman Ashik was left out of the playing eleven selected by Bino George as they retained a 4-2-3-1 shape. Syrian playmaker Khaled Alsaleh was flanked by Rohit Mirza and Vicky Meitei.
But the visitors were struck an early blow as Syrian playmaker Alsaleh was taken off the pitch in the tenth minute. Cameroon-born Francis Ambane was ushered in.
Mohammed Rafique's ambitious side-volley which ruffled feathers in the Gokulam defence in the early stages of the game but custodian Bilal Khan did well to track back and parry the effort over the bar.
Kamo Bayi and Ambane then turned up the heat as the latter's free-kick from range hit the crossbar after Luis Barreto was easily beaten off his line.
Kamo Bayi did well to beat a sliding Eduardo Ferreira challenge near the box but his shot, taken in haste from the edge of the box, was nowhere near the target in the 23rd minute.
For large periods in the first half, it was actually the visitors who controlled the game in midfield but the only goal of the game came against the run of play.
Left-back Santu Singh conceded a silly corner kick which could have been avoided but the hosts took maximum advantage as Mohammed Rafique hit a wonderful goal to break the deadlock.
Mahmoud Al Amna's corner-kick was punched out by Bilal Khan but Rafique, standing just outside the box, chested the ball down and sent the ball into the far corner on the bounce at the stroke of half-time.
Right after the restart, Kamo Bayi was taken off after his injury flared up again. Rohit Mirza was soon given his marching orders for a freak off-the-ball challenge on Katsumi Yusa. The former Mumbai FC man injured himself in the process. Katsumi Yusa then had to be replaced by the young Surabuddin Mollick.
Willis Plaza and Charles De Souza tried hard to find another goal but the Calicut-based side held on to the game well. Eduardo Ferreira tried a 'David Luiz' as he stepped up to take a free-kick from outside the box but the ball went flying into orbit.
With the win, the Red and Golds go level on points with Minerva Punjab but lead the table owing to a superior goal difference. They now travel to Imphal to face NEROCA FC on December 30.