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Chhangte scored two of City three late goals in a 3-2 win at Fatorda.
ISL: Mohun Bagan Super Giant beat Mumbai City to lift League Shield
With 45 points from 21 games, the Mariners are trailing top-placed Mumbai City FC by two points.
City won 2-1 to take their tally to 47 points while Mohun Bagan Super Giant are second on 42 points.
Lallianzuala Chhangte opened the scoring in a 3-0 win for Mumbai City.
The AIFF disciplinary committee found a March 8 complaint to be valid. The match had ended 1-1.
Mumbai City won 4-1 to take their points tally to 39.
City and Jamshedpur played out a 1-1 draw in the Indian Super League on Friday.
The West Coast Derby has often produced fireworks, but FC Goa has not won against Mumbai City FC in the ISL in over four years.
City are level on points with Odisha FC after a 2-0 win against Chennaiyin.