Boithang Hoakip, who replaced midfielder Eugeneson Lyngdoh, scored the opening goal for the hosts in the 63rd minute of the match.
A crowd of about 14,000 witnessed the match as the local outfit displayed enough discipline and skills to outsmart their fancied rivals.
What did not help Bagan's cause was that their foreign recruits -- Okolie Odafa and Tolgay Ozbey -