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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.
Mumbai City FC, Mohun Bagan Super Giant, FC Goa, Odisha FC, Kerala Blasters FC and Chennaiyin FC have qualified for the playoffs.
Chennaiyin jumped to ninth spot with 21 points from 19 games.
Bagan exploited Blasters' inexperience to pocket three vital points.
The visitors won 4-3 with Armando Sadiku scoring a brace.
The Mariners and their imperious frontline put on a full-throttle attacking showpiece in the first half where they hit the back of the net thrice to push the Red & Gold Brigade back early on in the proceedings.