Pakistan, leading the three-match series 1-0 after winning the first Test in Abu Dhabi, lost opener Shan Masood for 13 and Taufeeq Umar for 16.
At close Azhar Ali was four not out and with him Younis Khan on one, as Pakistan still trail by 369 runs.
Earlier New Zealand added 260 runs after resuming at 243-3, with Tom Latham scoring 137, Mark Craig made 43 and BJ Watling 39.
Left-arm spinner Zulfiqar Babar was the pick of bowlers with 4-137 while leggie Yasir Shah finished with 2-92 and seamer Ehsan Adil 2-73.