Brathwaite, nearing his fifth test century, shared gritty partnerships of 83 with Roston Chase (50) and Shane Dowrich (47) after West Indies had collapsed to 68 for four.
Darren Bravo was out for 12 before lunch, brilliantly caught by a diving Mohammad Amir off Zulfiqur Babar.
It was Amir's first test catch in his 20th match, the longest time any player has taken to get off the mark.
Pakistan hold an unassailable 2-0 lead in the series.
(Reporting by Ed Osmond, editing by Mitch Phillips)
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