Courage Pekuson pulled one back for the Blasters.
The win took Bengaluru to third position on the table and in touching distance of league leaders Chennaiyin FC.
The Blues could have easily scored more goals if not for some heroic goalkeeping by Subhasish Roy.
He was called into action a number of times on either side of the break, and he kept his team in the contest. Albert Roca's side were in complete control of the game from the start.
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The second half began much like the first. Roy was again called into action to save another Chhetri effort in the 50th minute.
But 10 minutes later, a hand-ball by Sandesh Jhingan gave Bengaluru a chance to take the lead from the spot. Chettri took the responsibility and this time Roy had no answers.
The game continued with Bengaluru looking more likely to score again than a reply from Kerala who were playing in front of their home supporters.
Barely a minute later, he got on to a cut back from Subasish Bose, who had done well to get inside the box after nutmegging Jhingan. Miku was left with a simple task of tapping the ball home, which he did with ease.
There was some consolation for Kerala as Pekuson scored with a down the middle sprint splitting the Bengaluru defence.