Japanese recruit Katsumi Yusa struck with a left-footer to the far post late in the 83rd minute to hand Mohun Bagan their first win against the bitter foes in two years, after six exchanges.
Mohun Bagan, who last won against East Bengal on January 7, 2012 in another local league exchange, finished with 25 points, three behind their arch-rivals.
Having taken an unassailable lead of 28 points after their 2-0 win over Kalighat MS in the last round, East Bengal had confirmed a record 35th CFL title with a match in hand.
It was Mohun Bagan, also sponsored by the UB Group, which impressed in the match with a standout performance by goalkeeper Shilton Paul.
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With Edeh Chidi and Ryuji Sueoka lurking in front, Paul saved Mohun Bagan the blushes. Mohun Bagan suffered a setback just after the first-half when ace striker Odafa Okolie pulled out after a hamstring pull.
With the Federation Cup beginning in less than a week's time, Odafa's latest injury will prove to be a big blow to their camp.