Resuming the second day on a strong 243-3, New Zealand lost Corey Anderson for nine in the second over of the day and then Latham in the third as Pakistan grabbed two wickets for just two runs.
When teams walked off for break, BJ Watling was 18 and with him Mark Craig was unbeaten on 13 as New Zealand's bids for a big total were thwarted by Pakistani bowlers.
Seamer Ehsan Adil (2-61) had Anderson caught in the covers before fellow new-ball partner Rahat Ali had Latham caught behind.
Latham, who scored 103 in New Zealand's 248-run defeat in the first Test in Abu Dhabi, fell in the next over as he edged a ball from Rahat to wicket-keeper Sarfraz Ahmed.
Latham failed to add to his overnight score of 137. He batted for 394 minutes and hit 11 fours and a six.
Jimmy Neesham added 33 for the sixth wicket with Watling before he miscued a drive off leg-spinner Yasir Shah and was caught at short mid-wicket by Misbah-ul Haq for 17.
Shah, who has figures of 2-70, could have another wicket but Rahat dropped a sitter at mid-wicket off Craig when the batsman was nine.
Pakistan lead the three-match series 1-0.