The win, which was sealed via the Duckworth-Lewis method, wrapped up the three-match one-day international series for the Kiwis 2-0.
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Batting first, after 30 overs the tourists had got themselves up to a respectable 215-3.
However, wickets then fell at regular intervals as Pakistan were bowled out for 290 inside 48 overs. Adam Milne was the pick of the bowlers, ending with figures of 3-49.
The hosts lost Brendon McCullum to a first-ball duck from Mohammad Amir in the second over, but the combination of Guptill (82) and Williamson (84) steadied the ship before both fell to the bowling of Azhar Ali.