Paceman Shannon Gabriel dismissed opener Azhar Ali and number three Asad Shafiq -- both for 0 -- off the second and fourth ball of the match after Pakistan won the toss and opted to bat at Sharjah stadium.
Opener Sami Aslam (37) and Younis Khan (39) were at the crease at the break after adding 80 to start building a recovery.
Pakistan are eyeing a series whitewash after winning the first Test in Dubai by 56 runs and the second in Abu Dhabi by 133.
Misbah started positively by winning the third toss in succession and instantly deciding to bat on a grassless and well rolled pitch.
But Ali, who scored a career-best 302 not out in the first Test, edged a lifting delivery from Gabriel after Sami had taken a single off the first ball.
Asad Shafiq also survived just one delivery before being trapped lbw. West Indian captain Jason Holder successfully challenged Australian umpire Paul Reiffel's not out decision.
Gabriel had figures of 2-22 at lunch.
West Indies also made two changes from the Abu Dhabi Test, with fit-again wicketkeeper Shane Dowrich replacing Shai Hope and paceman Alzarri Joseph coming in for Miguel Cummins.
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