At the interval Azhar Ali was unbeaten on 57 and skipper Misbah-ul Haq not out on 23 after Pakistan lost the in-form Younis Khan for 72 in the post-lunch session.
Pakistan still trail New Zealand's first innings total of 403 by 221 runs.
Pakistan lead the three-match series 1-0 after winning the first Test by 248 runs in Abu Dhabi.