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The result ensured the defending champions ended their campaign on 30 points from 18 matches.
Churchill, on the other hand, finished with 20 points from 18 matches, their position in the table to be decided at the end of the last matches of the tournament on Sunday.
Keeping an eye on the forthcoming Hero Federation Cup which kicks-off on May 7, Bengaluru coach Albert Roca preferred to rest a number of his star players.
Goalkeeper Lalthuammawia Ralte was handed his first I-League game with the Blues fielding just one foreigner -- defender Juanan pairing up with Sandesh Jhingan in central defence.
With the starting eleven boasting of five Under-22 players, the hosts surged into the lead as early as the fifth minute -- Gursimrat Singh swaying an inch-perfect cross from the right flank for Daniel Lalhlimpuia to tap it in.
A minute before conceding the goal, Churchill had bagged the first corner of the match which they failed to capitalise.
The visitors missed an easy chance to equalise few minutes later when Anthony Dsouza despite finding himself in a one-on-one with Bengaluru goalkeeper Ralte failed to make the most of it.
Meanwhile, some silky touches from the talented Udanta Singh puzzled Churchill defence. And it was the slippery Manipuri who doubled the lead in the 35th minute.
Grabbing a through pass, he cut in past the onrushing rival keeper Naveen Kumar, controlled it, and slotted it home as Bengaluru headed to the interval with a two-goal cushion.
Changing over, Churchill brought in striker Ansumana Kromah, in an effort to add more thrust in the attack. Both Kromah and his captain Anton Wolfe raided Bengaluru with solo efforts but an alert Bengaluru defence wasn't to be broken.
The final goal for the hosts came in the 84th minute as winger Mandar Rao Dessai curled it in off a pass from Salam Ranjan Singh.