Mohun Bagan are already out of the tournament and they are now at third spot with six points.
The defeat pushed Bengaluru FC down to second spot with nine points, behind Maziya Sports & Recreation of Maldives (12 points) who beat Abahani Limited Dhaka in Male earlier in the day.
Bengaluru now need to beat Maziya at home on May 31 in their final group match.
Only the group toppers advance to the knock-out stage from this South Asian Zone after the AFC completely overhauled the tournament rules.
With all eyes on the Federation Cup summit clash between the two teams on May 21, both sides retained only two players from the line-ups of their previous matches.
Mohun Bagan drew the first blood through Jeje Lalpekhlua in the ninth minute at the Rabindra Sarovar Stadium.
After leading 1-0, coach Sanjoy Sen further took off his forward Balwant Singh before the interval as the last season's I-League champions equalised through Seminlen Doungel (52nd) who ran solo before putting past an off the line Shilon Paul.
Bengaluru changed to a three-man defence with Gursimrat Singh Gill switching to centre-back but Mohun Bagan, playing their last match at home in front of a handful of supporters, dominated the proceedings and sealed the deal with goals from Kean Lewis and Bikramjit Singh in the space of six minutes.
Lewis beat the Bengaluru defenders at ease and looped over Lalthuammawia Ralte in the 74th minute to snatch the lead, while Bikramjit Singh completed the rout with a beauty in the 80th minute.
Having made the Federation Cup final, both the teams flew down from Cuttack to take part in the continental tier-two competition.
Sen made nine changes from the side that was in action against East Bengal in the Federation Cup with only Eduardo Fereira and Balwant being retained.
Bengaluru coach Albert Roca too had two men from the Federation Cup win against Aizawl FC as the Spaniard opted for an all-Indian eleven.
This was the two teams' fifth encounter this season with Mohun Bagan winning and drawing twice each. They will meet again in Cuttack in four days' time.
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