The bowlers and fielders combined to stifle Sri Lanka for runs and ensured that the visitors never looked capable of posing a challenge.
Chasing a reasonable 143 for victory, Kohli (30 not out) smashed a six in the 18th over to seal the deal for the rampaging hosts with 15 balls to spare.
Before the start of the match on Sunday, which was abandoned due to rain without a ball being bowled, the crowd sang Vande Mataram in absolute synchronization.
The ACA secretary said it was not expected that rain would play spoilsport at this time of the year.
India welcomed back Jasprit Bumrah and Shikhar Dhawan to the mix after both were out nursing respective injuries.
India lost the lung-opener by five wickets with Perera putting the inexperienced visiting attack to sword during his 37-ball 66.
While the Indian youngsters have put their hands up to deliver the goods, the Lankans are going through a terrible phase of transition.
Sri Lanka were reeling on 75/7 in their second innings when bad light forced the umpires to bring the curtains down on the match.
The Eden Gardens pitch has received rave reviews for facilitating an exciting Test match, where fortunes kept changing till the last hour.
Jasprit Bumrah's maiden five-wicket haul helped India to restrict hosts Sri Lanka to a modest 217 -9 in 50 overs in the third ODI.
With the series in the bag, the Indian skipper will be keen to complete 3-0 whitewash against Sri Lanka in the third Test at Pallekele.