Left-arm spinner Zulfiqar Babar took two wickets and paceman Rahat Ali one as New Zealand lost three key wickets after resuming at 15-0.
At the break Rod Latham was batting on 42 and with him Corey Anderson on 13.
The Kiwis still need 286 runs to avoid follow-on after Pakistan piled up a huge 56-3 declared in their first innings.
Brendon McCullum (18), Kane Williamson (three) and Ros Taylor (nought) were the batsmen out.
Babar has figures of 2-37 while Rahat has taken 1-1.-AFP