Resuming at 392-9 after lunch, Sarfraz Ahmed fell for 112 while Rahat Ali remained 16 not out.
They added 81 runs for the tenth wicket.
Pace partners Tim Southee finished with 3-67 and Trent Boult took 2-69.
Pakistan lead the three-Test series 1-0 after their 248-run win in the first Test in Abu Dhabi last week.