Chasing a target of 231 runs, the hosts were bowled out for 135 runs (39.5 overs) with youngster Karn Sharma picking three for 14.
Earlier, Kohli and Ambati Rayudu hit half-centuries before India were dismissed for a paltry 230 runs in 44.2 overs.
Kohli scored 71 runs off 75 balls, with eight fours and a six, while Rayudu retired out after scoring 72 runs, off 82 balls, with eight fours. The two batsmen put up 104 runs for the fourth wicket after the top-order had been dismissed cheaply once again.
Kohli led the side in the absence of MS Dhoni, though the team-sheets listed that all 17 players were once included in the match, with 11 batting and 11 fielding.
Shikhar Dhawan (10) and Rohit Sharma (8) were united at the top for India as they made a brisk start, scoring 19 runs in the first three overs. But then the brakes were applied as the two batsmen were dismissed within ten runs of each other.
Dhawan was caught at short mid-on in an attempt to clear the in-field while Sharma top-edged a catch to third man, albeit at the shortest boundary on the ground.
India were struggling at 52/3 in the 14th over when Kohli and Rayudu came together. They looked comfortable at the crease, although the stand-in skipper still seemed rusty from his poor show in the Test series prior.
They batted together for 16.3 runs and it seemed India were looking at a 250-plus score. But then Kohli was caught behind off left-arm spinner Ravi Patel (2-56) and that changed the complexion of the innings. Ravindra Jadeja (7) was sent up the order but he wasted this chance, holing out to deep mid-wicket in an effort to clear the ropes.
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