Mohun Bagan were trailing their arch-rivals 1-0 on December 9 in the eastern Indian city of Kolkata when one of their players was hit by a stone hurled from the stands.
The match resumed after a near 15-minute interruption but Mohun Bagan, founded in 1889, did not return to the field.
The All India Football Federation (AIFF) appointed a retired judge to look into the case and his finding got the approval of an I-League Core Committee on Saturday.
An AIFF statement said Mohun Bagan had been thrown out of the ongoing I-League competition, their matches had been declared null and void, and they would be disqualified from the next two editions of the league.
The club would also have to "return to the I-League any financial stipends that had been paid to it by I-League throughout the competition 2012-2013 or forfeit the right to the same," the AIFF said.
A revised fixture and points table would soon be issued, the AIFF added.
The I-League committee will decide on any possible additional sanction or fine in a January 9 meeting where the club would be asked to present its case.