Yusa Katsumi (45+4 minutes) opened the scoring from the penalty spot for the away side but Kivi Zhimomi (51st) restored parity.
An own goal by substitute Salam Ranjan Singh (87th) ensured East Bengal went back with a heavy heart.
Both captains, Arnab Mondal of East Bengal and Mohammed Irshad of Gokulam, were sent off in the second half added time.
Mondal picked up a second yellow for his lunge on Henry Kisseka while Irshad was given the marching orders for putting his arm on the face of East Bengal's Lalramchullova at the EMS Corporation Stadium.
Gokulam moved to the eighth spot with 16 points from 14 games.
East Bengal next take on Chennai City FC at home on February 24 while Gokulam will travel to Punjab to play Minerva on Tuesday.
Disclaimer: No Business Standard Journalist was involved in creation of this content
