Super sub Baljit Sahni gave a sloppy looking East Bengal the lead at the stroke of half time, while Lalrindika Ralte gave a two-goal cushion with a lucky 65th minute goal.
East Bengal could have easily added three more goals to their tally but Ralte and Sahni wasted opportunities galore.
The Goans were no better as they too squandered many chances before Beevan D'Mello reduced the margin in the 90th minute but it was too little too late as the loss almost ended the title hope of the fifth placed Sporting Clube de Goa who have 29 points from 20 matches.
Facing the difficult task of winning their remainder of matches, Armando Colaco began with Edeh Chidi upfront and Ryuji Sueoka behind against a defensive looking Oscar Bruzon side who had a packed midfield.
East Bengal had a lucky escape in the ninth minute when Joaquim Abranches almost deflected a Joseph Pereira cross into his own net as the red and gold brigade looked scrappy.
Coming in place of a lacklustre Cavin Lobo, Sahni almost scored two goals but his effort went in vain. He was third time lucky in the first half added time when his powerful strike hit the crosspiece before going into the net and the credit should be given to Abranches for his clinical cross.