Sri Lankan pace-cum spin attack put the brakes on Pakistan's progress after they resumed at 51-0.
They removed both the openers in the first hour and then made inroads on a still batting friendly Dubai stadium pitch.
They need another 177 more to avoid follow-on.
Pacer Lahiru Gamage took his first wicket in Tests when he bowled Shan Masood through the gate after the opener had made 16.
Sami Aslam was trapped leg before by off-spinner Dilruwan Perera for 39 to leave Pakistan two down for 65.
Asad Shafiq fell for 12 while Babar Azam made eight.
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