Williamson, who has had an indifferent tour so far, struck a fluent 118 off 128 balls with 14 boundaries and a six. However, save opener Tom Latham (46), none of the other batsmen could provide considerable support.
The last 15 overs of the innings yielded only 66 runs for the Black Caps.
While Amit Mishra (3/60 in 10 overs) picked up the important wicket of Williamson, it was Jasprit Bumrah (3/35 in 10 overs) whose bowling was a revelation during death overs.
In all, Bumrah bowled an astounding 37 dot balls in his 10 overs while the entire team bowled 161 in all which is equivalent to 26.5 overs without scoring.
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Umesh Yadav (1/42) started with a perfect delivery that pitched on the middle and knocked off Martin Guptill's (0) as off-stump.
However, Williamson looked confident from the outset as he timed his shots to perfection. He had an able ally in Latham and they put on 120 runs for the second wicket in 20 overs at a fair clip.
Williamson pulled a short ball from Bumrah and a deliberate slash over slips to collect a couple of more boundaries.
When Axar Patel was introduced into the attack, his short ball was promptly dispatched to the mid-wicket boundary and then the skipper came down the track to loft him over long-on.
To add insult to the injury, he used the pace of the next delivery to guide it past gully for a boundary.
At 46, Pandya dropped a low catch off Bumrah's bowling and then swept Mishra to complete his half-century with a boundary.
It was Kedar Jadhav, who bowled one full, and Latham missed the line to be adjudged leg before. His run-a-ball 46 comprised six boundaries and a six.
Ross Taylor (21) looked out of sorts during his 42-ball stay at the wicket before trying to hoick Mishra only to be caught by Rohit Sharma at mid-wicket fence.
Williamson continued to bat confidently as he hooked Pandya to enter the 80s. However, the Kiwi skipper slowed down a bit during this phase where Corey Anderson (21) joined him.
The genial Kiwi skipper got a generous applause from the capacity Kotla crowd.
Williamson lost Anderson after a 46-run stand as Mishra picked up his second wicket. It was a flipper and Anderson trying to play off the backfoot missed the line completely.
The New Zealand skipper was finally out on 118 when he tried to up the ante by hitting Mishra down the ground but Rahane standing at long-off boundary moved sideways to his right to take a well-judged catch.
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