The Black Caps then bowled out India for 296 in 46 overs despite Kohli’s 54th ODI century and clinched the three-match series 2-1.
New Zealand had lost all seven of their previous ODI series in India, a run dating back to 1988.
The Black Caps registered their first ever Test series win in India with a 3-0 sweep in October 2024, and added another landmark success in this series despite being without several key players including Kane Williamson, Mitchell Santner, Tom Latham, Rachin Ravindra and Jacob Duffy.
“We’re the sum of all the parts and we really try to work together as a group – that’s part of the Kiwi way,” captain Michael Bracewell said.
“We’re just a small country from the bottom of the world and we try to work together to take on some of the bigger countries in the world.”
He added: “We really rally around there as a group and when things come like that, it’s pretty special.”
India – the world’s most populated nation with 1.4 billion people – are the top-ranked ODI side ahead of New Zealand.
The in-form Kohli, who plays just the 50-over format after retiring from Test and T20 international cricket, threatened to pull off a remarkable chase in a 99-run seventh-wicket partnership with Harshit Rana, who made 52.
New Zealand left-arm spinner Jayden Lennox returned figures of 2-42 from his 10 overs after Bracewell left the field with a calf injury and did not return.
Mitchell led the team in Bracewell’s absence, which also left New Zealand a bowler short.
Zak Foulkes and fellow seamer Kristian Clarke took three wickets each.
New Zealand players celebrate after winning the third ODI at the Holkar Cricket Stadium in Indore. Photo / AFP
India slumped to 71-4 before Kohli hit back in an 88-run stand with Nitish Kumar Reddy, who made 53, and then with Rana.
“The way Virat is batting, that’s definitely a plus always,” said India captain Shubman Gill. “The way Harshit has batted in the series, batting at number eight, it’s not easy.”
Kohli struck 10 fours and three sixes in his 108-ball knock before he was caught off Clarke and walked back to a rousing ovation after his 85th international century.
Earlier the in-form Mitchell picked up from where he left off after his match-winning 131 not out in the second ODI, which levelled the series at 1-1.
Mitchell reached his ninth ODI ton with a single off Ravindra Jadeja before Phillips also brought up his hundred.
Arshdeep finally dismissed Phillips caught behind to end the marathon stand and Mitchell soon followed, falling to Mohammed Siraj.
Mitchell was named player of the match and series for his 352 runs in three matches.
New Zealand wobbled, losing four more wickets but Bracewell hammered an unbeaten 28 off 18 balls.
The teams next play five T20 matches in a final tune-up for the T20 World Cup in India and Sri Lanka between February 7 and March 8.