"After 11 years the Football I-League trophy comes back to #Bengal. Congratulations Mohun Bagan," Banerjee posted on the micro-blogging site Twitter.
In the final league match, Bagan went down by a goal in the first-half.
After the lemon-break, they regrouped and netted the equaliser towards the closing minute via a header of Nigerian defender Bello Rasaq giving the national club of the country its fourth national title.
Last time, the green and maroon brigade won the title, then called the National Football League, in 2002.