The result set Gokulam on the right path in their quest to win a hat-trick of titles in the I-League.
The win took the Malabarians two points clear of Mohammedan Sporting (25) in the 13-team standings.
Emil Benny was sent off shortly after Rahim Osumanu scored for the defending champions.
Former Shakhtar Donetsk U21 player Gabriel Lima Silva has signed a season-long deal with Malappuram-based second division club Kerala United FC
Both Gokulam and Churchill ended up tied with 29 points, but Gokulam emerged champions on head-to-head record.
The Malabarians have become the first team from Kerala to win the I-League title.
Gokulam is attempting to become the first Kerala team to win the I-League title.
The title will now be decided on the last day of the season with three teams -- Gokulam, Churchill and TRAU -- in contention to lift the trophy.
Churchill Brothers survived a last-minute scare to beat 10-man Gokulam Kerala FC 3-2 and extend their lead atop the I-League table.
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.