New Zealand won the series 3-2.
Williamson fell three runs short of a second successive century as he and Ross Taylor (88 not out) led New Zealand to a formidable total of 275 for four at the Sheikh Zayed Stadium.
The Kiwis then bowled out Pakistan for 207 in 43.3 overs thanks mainly to paceman Henry (5-30) who was named man of the match.
Pakistan's chase got off to a poor start when Henry trapped opener Nasir Jamshed leg before for a duck.
Haris Sohail (65) and Ahmed Shehzad (54) rallied with half-centuries but their team struggled to recover from the early breakthroughs made by Henry, who also removed Younis Khan for 12.
Opting to bat in the decider, New Zealand lost Martin Guptill in the third over before the in-form Williamson, voted the man of the series, added 66 runs with Dean Brownlie (34).
Left-arm spinner Zulfiqar Babar trapped Brownlie leg before but Pakistan had to wait another 23 overs to celebrate another dismissal as Williamson and Taylor added 116 runs for the third wicket.
Shahid Afridi denied Williamson his second century in a row when he fluffed a sweep shot and was caught.
Pakistan bowled with discipline but Taylor and Tom Latham (22 not out) helped New Zealand hit 85 in the last 10 overs.
Image: Kane Williamson
Photograph: Francois Nel/Getty Images
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