Pakistan had reached 87-2 at lunch, with Shoaib Malik unbeaten on 37 and Younis Khan on 21 not out, after they won the toss and chose to bat on a grassless pitch at the Sharjah stadium.
Malik, who hit a career-best 245 in the drawn first Test in Abu Dhabi, successfully challenged Australian umpire Bruce Oxenford's leg-before decision off spinner Moeen Ali when he was on 22.
He took 20 balls to score his first run but has hit five boundaries so far.
Mohammad Hafeez swept Moeen Ali's first delivery to the boundary but miscued a pull shot and was caught in the deep by Stuart Broad for 27.
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Pakistan, leading the series 1-0 after their 178-run win in the second Test in Dubai, brought in Azhar Ali and paceman Rahat Ali, dropping Shan Masood and the injured Imran Khan.
England were forced to leave out seamer Mark Wood with an ankle problem and dropped the out-of-form wicketkeeper-batsman Jos Buttler, including slow left arm spinner Samir Patel and batsman James Taylor.