With their second loss from as many games in the five-match series, India slip to second in the rankings, dropping two points to 117.
Australia - sitting on 118 on the back of their 3-0 ODI series-winning lead over England - move up to No.1, with South Africa third (110), followed by Sri Lanka and England (108), Pakistan (101) and New Zealand who improve one place to seventh on 90.
India were chasing a Duckworth-Lewis revised total of 297 after New Zealand reached 7-271 from their allocated 42 overs when rain stopped play for nearly two hours earlier in the day.
The match finished three balls short of 42 overs after rain set in, with India on 9-277.
The 15-run win gives the Black Caps a 2-0 lead after Sunday's 24-run victory in the first ODI in Napier.
India looked on target for the win, but a superb Kiwi bowling performance snared the key wickets of Virat Kohli and MS Dhoni late in the innings to smother the run chase.
Corey Anderson, who also featured with the bat, picked up two wickets in four balls in the 40th over to finish with figures of 3-67, including the wicket of Dhoni for 56 off 44 balls.
But the key performance came from Tim Southee, who removed Kohli for 78 on the way to becoming the 15th New Zealand bowler to take 100 ODI wickets. He finished with 4-72 off nine overs.
Southee also accounted for both Indian openers, yorking Shikhar Dhawan midway through the eighth over for the initial breakthrough with the score on 22.
And when Rohit Sharma clipped a faint edge to keeper Luke Ronchi for 20 late in the 10th over, India were 2-37 as Southee notched up his 100th ODI wicket in 76 matches.
Earlier, another whirlwind innings from Anderson blasted the Black Caps to a competitive total.
Anderson continued on from his unbeaten 68 in Napier and a 36-ball century against the West Indies in the New Year's Day ODI.
The 23-year-old left-hander belted 44 off 17 balls, stroking two boundaries and sending five sixes into the Seddon Park crowd.
Kane Williamson, with a more-measured 77 off 87 balls, and Ross Taylor (57 off 56) provided the mainstay of the New Zealand innings, along Martin Guptill who put on 89 runs for the second wicket in his 65-ball 44.
Anderson's dismissal with one ball remaining in the 39th over, skying a slower ball from Ishant Sharma to Dhawan at long on, signalled something of a mini-collapse.
Brendon McCullum (0), Taylor and Nathan McCullum (1) all disappeared in the space of six balls before Ronchi's breezy 18 off 10 balls eased the Black Caps home.
The third game is scheduled for Eden Park in Auckland on Saturday.