The all-rounder clubbed seven fours and seven sixes on the way to his maiden one-day century to help the hosts overhaul New Zealand's challenging 7-315 with seven balls to spare at the Chinnaswamy Stadium in Bangalore.
The victory put India on course for a series whitewash over the Black Caps who trail 4-0 with one game remaining to be played in Chennai on Friday.
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Pathan clobbered the New Zealand attack with his aggressive innings, putting on 133 runs for the unfinished sixth wicket with Saurabh Tiwary (37 not out) after India had been reduced to 5-188 in the 34th over.
Pathan also played a key role with the ball, grabbing three New Zealand wickets for 49 runs off nine overs.
James Franklin top-scored for the Kiwis with an unbeaten 98 off 69 balls including 12 fours and three sixes.
"I have always said Pathan can finish games on his own, and that's what he did today," Indian captain Gautam Gambhir said.
"I had never seen something like this before. But I knew till the time Pathan was there, we would win the game."
Paceman Andy McKay took two wickets in two balls to spoil a rollicking start by India that saw openers Gambhir (27) and Parthiv Patel put on 67 runs in less than 10 overs.
Gambhir, the leading run-getter in the series, cut McKay to point where Martin Guptill took a sharp catch and Virat Kohli was caught by Kyle Mills for a duck.
Patel, playing his first one-day international in six years, raced to his maiden one-day half-century off 50 balls but was dismissed three runs later by Nathan McCullum.
India looked in deep trouble after losing Yuvraj Singh for 20 runs but man of the match Pathan ensured another fine win for the hosts.
"It was a great game of cricket," said New Zealand skipper Daniel Vettori.
"We were in the game, but Pathan was pretty amazing. Franklin played exceptionally well too to give us a formidable total, but Pathan took the game away from us."
Franklin had underlined a spirited batting display by the visitors after they were put in to bat in the day-night game. Scott Styris (46), Ross Taylor (44) and Brendon McCullum (42) also chipped in with valuable knocks.
Franklin, who had top-scored with 72 in the third match in Vadodara, provided the late impetus, helping New Zealand add 63 runs in the last five overs.
He hit two sixes and as many fours in the last over by Ashish Nehra (2-70) to take the visitors past the 300-run mark.
