The Black Caps made 212 for four, with Colin Munro top-scoring for the hosts with 72 off 40 balls.
After being asked to bat, New Zealand demolished the Indian bowling attack to post an imposing 212 for four in their allotted 20 overs.
A New Zealand XI has beaten Bangladesh by two wickets in a one-day match at Lincoln.
Meanwhile, Indian bowlers too showcased an impressive performance, with Krunal Pandya bagging three wickets and Khaleel Ahmed, Hardik Pandya and Bhuvneshwar Kumar sharing four wickets among themselves to restrict the hosts for 158. After losing his opening partner, Rohit Sharma built a crucial partnership with Vijay Shankar.
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The Black Caps ended India's run of 10 Twenty20 global series without a defeat.
Shikhar Dhawan fell early in the India reply but Rohit Sharma (38) and, in particular, Vijay Shankar (43) kept the tourists up with the required rate.
Colin Munro struck a 40-ball 72 as New Zealand pipped India by four runs in the third and final Twenty20 worldwide at Hamilton to seal a 2-1 series victory on Sunday.
On the third ball of the final over, Karthik denied a single and later ended up taking a single off the next ball.
India will have another chance to shore up their options in the ODI series against Australia which will begin towards the end of this month. With the scoreboard pressure mounting, the two batsmen next, Dinesh Karthik and Krunal Pandya did their best as they scored 18 and 14 runs off the eighteenth and the nineteenth overs respectively.