The hosts finished at 196-5 with Asad Shafiq (41) and Sarfraz Ahmed (24) were at the crease with Pakistan falling 65 short of the target at the Dubai International cricket stadium.
Pakistan lead the three-match series 1-0 after winning the first Test by 248 runs in Abu Dhabi.
Ross Taylor hit a brilliant 104 to help New Zealand declare their second innings at 250-9.
Leg-spinner Yasir Shah took his first five-wicket haul with 5-79 and left-armer Zulfiqar Babar took 4-96.
The third and final Test begins in Sharjah from November 26.
Complete scoreboard on the fifth and final day of the second Test between Pakistan and New Zealand at Dubai International Cricket stadium on Friday is as follows,
New Zealand 1st innings 403 (T. Latham 137, M. Craig 43; Zulfiqar Babar 4-137)
Pakistan 1st innings 393 (Sarfraz Ahmed 112, Azhar Ali 75, Younis Khan 72; T. Southee 3-67)
New Zealand 2nd innings 167-6 (R. Taylor 104, B. McCullum 45 ; Yasir Shah 5-79)
Pakistan 2nd innings (Younis Khan 44, Azhar Ali 24; Boult 2-12)