Shafiq drove paceman Shannon Gabriel to cover boundary for his sixth boundary to complete his 16th half-century to lift Pakistan after Misbah-ul-Haq won the toss and opted to bat on a flat Sheikh Zayed Stadium pitch.
After an extended two-and-a-half hour extended session due to Friday prayers, Pakistan were 95-2 with Shafiq on 54 and with him Younis Khan on 29 not out.
The normal red ball and daylight cricket returned in Abu Dhabi after the first Test was a day-night affair with the pink ball in Dubai, as Pakistan were off to an unimpressive start.
Sami Aslam also did not last long as he missed an ambitious drive off leg-spinner Devendar Bishoo and was bowled for six.
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Shafiq was at his best from the start, playing with confidence as he has so far hit six boundaries in his 90-ball stay.
Younis, who missed the first Test due to recovery from dengue fever, has so far hit a single boundary.
Pakistan, who leads the three-match series 1-0 after winning the first Test in Dubai by 56 runs, brought in Younis, Zulfiqar Babar and Rahat Ali in three changes to the first Test line-up.
West Indies were forced to leave out unfit wicket-keeper batsman Shane Dowrich, bringing in Shai Hope.
The third and final Test starts in Sharjah from October 30.
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