For Mohun Bagan, who is on the top of the table, it was the first time they were defeated in the present Hero I-League tournament.
Joel Sunday of the home team scored the first goal at the beginning of the match, while Mohun Bagan's Glen scored the equalizer in the 24th minute after which Chhawnkima of AFC shot the winning ball in a penalty.
AFC Captain David Rinmuana was awarded 'Hero of the Match' for the fourth time.
With this AFC has played 12 matches and bagged 12 points to hold seventh position in the table.
Have not decided on retirement: Afridi
Whole team in state of sorrow after India loss: Mashrafe
Can't always use 'transition phase' as an excuse: Chandimal
PHOTOS: Team India, Australia's Maxwell celebrate Holi
AFC Cup: Mohun Bagan thrash South China; Bengaluru FC lose