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.
Gokulam improved their tally to 10 points from seven matches with the win.
Twelve teams are in the fray.