Set a target of 169, Guptill finished the match with a boundary to take the New Zealand total to 171 with 14 balls remaining and all wickets intact.
His stand with Williamson eclipsed the previous best Twenty20 partnership of 170 set by South Africans Graeme Smith and Loots Bosman against England in 2009.
New Zealand's dominance in Hamilton, after Pakistan won the first game in Auckland on Friday, means the three-match series will be decided in Wellington next Friday.
Williamson faced 48 balls for his 72, which included 11 fours.
Pakistan won the toss and elected to bat first but there was no urgency about their run-gathering.
Halfway through their innings Pakistan were 60-2, while New Zealand passed the same 60 mark in the seventh over and were 82-0 after 10 overs.
Williamson and Guptill both brought up their half-centuries in the 13th over when they took 15 off Mohammad Amir, whose three overs cost 34 runs.
After the slow start to the Pakistan innings, Umar Akmal and Malik added backbone with a 63-run partnership off 34 balls to get the tourists up to 168-7.
Akmal was unbeaten on 56 off 27 deliveries at the close while Malik made 39 off 30.
New Zealand, with an eye on the World Twenty20 in India in March, experimented with left-arm spinner Mitchell Santner opening the bowling. New-ball spearheads Trent Boult and Matt Henry sat out the match.
But when Santner was removed from the attack, Corey Anderson and Adam Milne put the brakes on the scoring before the Akmal-Malik onslaught.
While Pakistan only scored 60 runs in the first 10 overs, they added 108 in the second half of the innings.
Mitchell McClenaghan had the best figures for New Zealand with two for 23.
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