The match resumed after a 13-minute stoppage towards the end of the first half, but Mohun Bagan refused to take the field after the interval as Nabi, an India international, was treated for a fractured right jaw.
The Kolkata-based Telegraph newspaper quoted police as saying that 45 people, including seven policemen, were injured as fans disrupted traffic and stoned cars outside the Salt Lake stadium.
Some 85,000 fans attended the match at the 100,000-capacity venue.
Sunando Dhar, chief executive of India's top division the I-League, said tournament rules stipulated that a team could be banned for three years for refusing to take the field.
"Having played until half-time, Mohun Bagan could be suspended from the current season and the following two seasons for not agreeing to continue the game," Dhar said.
The I-League committee is expected to decide Mohun Bagan's fate before their next match against Pailan Arrows on December 15, the Telegraph said.