The New Zealand XI, in reality a shadow Test team, were 111 for four when stumps were pulled, an overall lead of 208.
Pakistan conceded a 97 run lead to the New Zealand XI, who made 384 in their first innings led by Brendon McCullum’s 206 from 218 balls.
After the hosts posted 384 in their first innings, Pakistan recovered from a woeful start, when they were 39 for four, to be all out for 287.
Misbah, who did not play in the recent Twenty20 series, earned valuable time in the middle with an unbeaten 126 in nearly six hours at the crease.
The next best score for Pakistan was 35 by wicketkeeper Adnan Akmal.
Seam bowler Umar Gul, who took three wickets in the first innings, continued his form in the second with the dismissals of Brendon McCullum and Kane Williamson in the space of three balls, to end with two for 19.
The first Test in the two-Test series between New Zealand and Pakistan starts in Hamilton on Thursday.