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Mohun Bagan's matches in the competition are now null and void with the club 'considered to have withdrawn,' the AFC said in a statement.
Thaer Krouma scored a late equaliser as City came back from 0-2 to make it 2-2.
Anwar Ali, East Bengal and Delhi FC, are all jointly 'iable' for the compensation amount.
Kerala Blasters' latest signing Noah Sadaoui takes the Golden Boot.
The goalkeeper made doubles saves in tie-breaker as the defending champions won 4-3.
The loss also crushed Mohun Bagan's dream of becoming the first team to defend the ISL Cup and complete a rare double of winning the League Winners' Shield and the title.
The goal came just when the match was meandering towards extra-time as the 62,000-plus capacity crowd at the Salt Lake Stadium erupted in joy.
The Juggernauts thus secured their first-ever ISL win over the Mariners after nine attempts, as a game of close margins kicked off amid frenetic circumstances with all three goals being netted in the first-half of this match.
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.
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