Kerala, who were looking to keep themselves in contention for a play-off berth before the match, could not convert the chances that came their way.
Miku struck the first goal in the 91st minute and Udanta Singh found the net in 94th.
The top-scorer for Bengaluru, Miku scored his 14th goal of the season after he charged into the box and slotted past Kerala goalkeeper Rachubka.
Udanta scored after cutting into the box off Dimas Delgado's pass from the right, before sending a powerful kick into the corner of the net.
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There were some anxious moments too, especially when Bengaluru head coach Albert Roca kicked the ball away in anger as referee gave a throw-in to Kerala Blasters.
The coach was warned by the referee in the 44th minute.
One of the best chances for Bengaluru came in the 75th minute when Udata headed the ball wide after Dovale picked the Indian winger.
In the 45th minute, Bengaluru FC called for penalty, but was denied by the referee after Miku had cut onto his left foot before falling over.
In the 23rd minute, Bengaluru had another chance to score but the rival defender shot the ball over after Nishu Kumar failed to reach the ball, which was deflected into his path off Chhetri's foot.
Haokip then pierced a powerful long ranger, which was wonderfully saved by Rachubka.
Even the rivals had their chances, especially in the 37th minute when Milan aimed a freekick towards Jhingan, who got his head to the ball but was unable to direct it towards the goal.
In the 62nd minute, Dovale slipped in Chhetri and the skipper blasted his shot over from a tight angle.
Malayali flavour came into play in the 71st minute as Rino Anto whipped in a teasing cross into the box from right for Vineeth to head, but not before Gurpreet Singh Sandhu jumped higher than the forward to palm the ball away to safety.