Philip Adjah Tettey scored in the 68th minute of the game which was completely dominated by Gokulam.
With the result, the Punjab side have now displaced Churchill Brothers on the summit of I-League points table with 14 points from eight outings — one point ahead of the Red Machines, who have played one game less.
A Jiteshwor Singh own goal, strikes by Philip Adjah and Jestin Geroge and Mohammad Sharif's penalty were enough to hand the Malabarians three points and put them in the top half of the standings.
I-League 2021: NEROCA FC Judah Garcia scores brace in 4-0 win over Indian Arrows, Aizawl FC beat Gokulam Kerala
Varney Kallon and Khaiminthang Lhungdim also scored a goal each as NEROCA bagged their first win of the season.
I-League 2021: Gokulam Kerala fight back to beat Punjab FC in seven-goal thriller; Churchill Brothers hold Mohammedan
In a tactical match where chances were few and far between, both teams cancelled each other out in the middle of the park, sharing the spoils of the match.
Vijay Naggapan's 50th-minute strike proved to be the difference between the two sides after Gokulam Kerala's third-minute strike by Dennis Antwi was cancelled out by Elvedin Skrijelj's 26th-minute penalty.
With the latest edition of the I-League set to begin on 9 January, Gokulam Kerala FC began their pre-season training in a controlled environment amid the COVID-19 pandemic
Coronavirus Outbreak: Lockdown has brought everyone together, says Gokulam Kerala's Afghan midfielder Zohib Islam Amiri
Stranded in India due to the coronavirus-forced travel restrictions, Gokulam Kerala FC's Afghan recruit Zohib Islam Amiri feels the lockdown has brought everyone together, preferring to remain positive by spending hours on phone with his family.
Priya has joined the same helpline centre in Kannur, where India and Jamshedpur FC attacker CK Vineeth has been working.
I-League 2019-20: Henry Kisekka last-minute goal for Gokulam Kerala dents Churchill Brothers' hopes of second place finish
Henry Kisekka scored in the last minute as Gokulam Kerala FC beat Churchill Brothers 2-1 in a thrilling match of the I-League on Sunday.
I-League 2019-20: Gokulam Kerala FC score late equaliser through Nathaniel Garcia to hold second-placed Punjab FC
Gokulam, who have not been too solid in defence so far this season, were on their toes trying to stop Punjab's counter-attacks
I-League 2019-20: Hosts Neroca FC escape dropping into relegation zone with 3-2 win over Gokulam Kerala
Hosts Neroca FC eked out a narrow 3-2 win over Gokulam Kerala FC in their I-League clash to come out of the relegation zone.
Back in their own backyard, East Bengal will host Kerala outfit Gokulam Kerala FC in a must-win I-League match for both the teams on Wednesday.
Gokulam Kerala FC played out a 1-1 draw against 10-man Aizawl FC in an I-League match at the EMS Stadium on Saturday.
I-League 2019-20: Real Kashmir's upcoming home fixtures delayed after inclement weather forces closure of Srinagar airport
Real Kashmir FC's two upcoming home I-League matches were on Monday postponed owing to inclement weather which has forced closure of the Srinagar airport, the All India Football Federation (AIFF) said.
I League 2019-20: Solitary Henry Kisekka goal sees Gokulam Kerala FC get the better of Indian Arrows
Gokulam coach Valera played both Kisekka and Trinidadian captain Marcus Joseph upfront while Arrows' new coach Shanmugam Venkatesh also began with a regulation 4-4-2, with Vikram Partap Singh and Aman Chetri upfront.
Durand Cup 2019: Marcus Joseph's hat-trick propels Gokulam Kerala FC into semi-final with win over TRAU FC
Marcus Joseph struck in the 59th, 64th and 83rd minutes with the second one coming through a penalty in Gokulam Kerala's final Group D match.
Durand Cup 2019: East Bengal first team to seal semi-final berth; FC Goa, Gokulam Kerala win to remain in hunt
Gokulam Kerala's Trinidad and Tobago playmaker Marcus Joseph once again did the maximum damage, striking a double (43rd, 87th) while Shibil Muhammed scored in the 56th minute to fashion a 3-0 win over Indian Airforce at the Sailen Manna Stadium in Howrah
Mohun Bagan had no trouble against ATK, as Joseba Beitia set up one for Fran Morante in a 34th-minute corner kick and struck another in the 53rd minute to earn a 2-1 win.
In a letter signed by Swapan Sadhan Bose, managing director of Mohun Bagan, the I-League clubs have urged the prime minister to "intervene and save the sport".