Batting first, the Black Caps recovered from a top-half collapse to post 262 for the loss of seven wickets - boosted by the efforts of James Franklin (62) and Nathan McCullum (53 not out).
The momentum swung both ways in the second innings, with Ahmed Shehzad (42) and Younis Khan (42) chipping in alongside Misbah, but New Zealand were able to maintain the run-rate pressure on their opponents.
Scott Styris picked up three wickets while skipper Daniel Vettori and Hamish Bennett grabbed two wickets each, but in the end Misbah's heroics propelled the visitors towards a 2-1 lead in the six-match series with two left to play.
Earlier in the day, Pakistan ripped through the New Zealand top order inside 10 overs to send back Martin Guptill (21), Jamie How (13) and Ross Taylor (four) with Wahab Riaz and Abdul Razzaq sharing the spoils.
The hosts' woes deepened with Scott Styris (11) being run out, while Mohammad Hafeez snapped up Kane Williamson for 15 - caught at midwicket by Younis Khan.
Franklin and Brendon McCullum then managed a steady 50-run sixth-wicket stand, but Riaz removed the latter after his quickfire 37.
Franklin proved to be a face saver for the hosts, smashing three boundaries off Sohail Tanvir to reach his fifty, but skipper Shahid Afridi ended his run - and the 64-run stand he had built with Nathan McCullum - with a catch by Riaz at backward square leg.
Nathan McCullum blasted five boundaries and a six during his 58-ball innings as he and Vettori (13 not out) held a 57-run partnership to round up proceedings.
Pakistan's start was emphatic with Ahmed Shehzad leading the way, but Mohammad Hafeez's (12) slash at a Bennett delivery was caught brilliantly by Taylor at slip.
Shehzad looked in fine touch, smashing six boundaries and a six, but the Kiwis stemmed the run flow as a combination of Styris and Taylor resulted in two quick wickets.
Shehzad and Kamran Akmal (20) both misjudged Styris' slower deliveries within four overs of each other and lobbed simple catches to Taylor at short midwicket.
Younis and Misbah cautiously took their partnership past 50 without a boundary being hit - the first coming 76 balls into the fourth-wicket stand.
Both batsmen were nearly neck and neck in their individual scores, with Misbah reaching his half century first, but Younis was then run out left stranded off his crease and eight short of his fifty.
With the asking rate ever increasing, Pakistan stumbled again as Vettori removed Umar Akmal (10) and Afridi (four) in the same over.
Misbah gave the visitors plenty of hope with his aggressive play. And despite the dismissals of Razzaq (23) and Riaz (nought), Sohail Tanvir (14 not out off six balls) eventually took Pakistan over the line, hitting three boundaries in the penultimate over to snatch victory for his side.