Emil Benny was sent off shortly after Rahim Osumanu scored for the defending champions.
Hyderabad FC thumped Assam Rifles 5-0 in another Group D match.
Hyderabad FC failed to qualify for the play-offs after being held by the Gaurs.
Trailing twice in a high-pressure clash, leaders ATK Mohun Bagan fought their way back and played out a thrilling 2-2 draw against 10-man Hyderabad.
The result meant Kerala Blasters are out of the play-off race.
With the draw, Hyderabad are at third spot with 24 points from 17 matches while SC EB are at ninth with 17 points from as many matches.
While Hyderabad moved to third on goal difference, NEUFC climbed above FC Goa to fourth.
Hyderabad FC beat Chennaiyin FC 2-0 in the early kick-off to move up to third.
Aridane Santana pulled one back in the 86th minute before Fran Sandaza scored a 90th-minute equaliser as BFC's winless run extended to eight games.
Halicharan Narzary put Hyderabad ahead at the break but saw his header cancelled out by Cole Alexander in the second half.