Nishu Kumar and Marjan Jugovic scored in the 40th and 83rd minutes in the Group E match at the Kanteerava Stadium.
With this win, Bengaluru remained on top of the group with nine points from three matches. It was Abahani's third loss in as many matches and they remained at the bottom of the group.
The 3-4-3 formation worked beautifully for Bengaluru as the wingbacks dominated the game.
Nishu aimed perfectly past Abahani goalkeeper's reach in 40th minute. He took full advantage of a beautiful short- passing move among Harmanjyot Khabra, Sunil Chhetri and Daniel who released the ball for Nishu, who did not make any mistake.
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Bengaluru also had a few other close chances, especially in 12th minute when Len attempted a diving header but could not keep it down in front of a empty net.
Abahani, on the other hand, had their best chance in the 33rd minute when Ziban got the better of Ranjan and Juanan. But Ralte denied him a goal.
Again in 33rd minute, Abahani spilled another scoring chance when Mamun could not reach to a pass of Brown as Nishu intercepted the dangerous move.
Khabra missed a wonderful chance for Bengaluru in the 60th minute when he shot straight into hands of goalkeeper Shahidul.
In the 68th minute, Chehetri sliced it past Abahani keeper Shahidul but Mamun pulled off a stunning goal-line clearance.