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Jeje Lalpekhlua (9th minute) handed Mohun Bagan the early lead before Seminlen Doungel (52nd) pulled BFC level.
However, Kean Lewis (74th) and Bikramjit Singh (80th) scored for Mohun Bagan in the late stages to ensure that the sparse home crowd went back happy.
With both teams scheduled to meet bin the final of the Federation Cup on Sunday, they preferred to rest their top players.
Table toppers Maziya Sports and Recreation Club blanked bottom dwellers Dhaka Abahani 2-0 at home in the other Group E match on Wednesday to consolidate their position at the top of the heap.
Mohamed Umair (59th) and Aleksandar Rakic (85th) scored for the Maldivian outfit at the National Stadium in Male.
Maziya , who have won four of the five matches they have played so far, are currently on 12 points. They have already qualified for the next stage of the competition -- the inter-zone play-off semi-finals.
Bengaluru remain on nine points from five matches which include three wins and two losses. They needed to win on Wednesday as well as their last group game against Maziya on May 31 to have chance of taking pole position advancing to the next stage.
However, the defeat to Mohun Bagan extinguished their chances as even if they beat Maziya, the reigning Maldives will go through on account of their superior goal difference.
Mohun Bagan, who had already crashed out of contention, are at the third spot with six points from five matches.
With Mohun Bagan and BFC scheduled to meet in the final of the Federation Cup on May 21, both teams largely fielded second string line-ups.
Both line-ups included only two players from the Federation Cup semi-finals. While Mohun Bagan fielded striker Balwant Singh and Brazilian defender Edu, BFC retained Salam Ranjan and C.K. Vineeth.
Mohun Bagan enjoyed the stronger start and took the lead when a delightful chip from Raynier Fernandes from the mid-field found Jeje Lalpekhlua with plenty of time and space near the BFC penalty box.
Jeje made full of some lax defending to beat BFC goalkeeper Lalrindika Ralte.
Jeje got another chance in the 15th minute when an acccurate long ball found him unmarked near the BFC penalty box. But he smashed the ball over the bar despite having lots of space.
The hosts wasted several chances before the break and paid for their mistakes when Doungel latched onto a pass from Daniel Lalhlimpuia to score the equaliser.
However, Lewis ensured that the hosts regained the lead when he was found by a through by Bikramjit.
Bikramjit then completed the tally with a superb strike. Picking up the ball in the midfield, he gave a lovely lofted through ball towards the left wing which was picked up by Lewis.
Lewis' shot at the goal was blocked but Bikramjit pounced on the rebound just outside the penalty box to beat Ralte with an accurate shot.
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