Opener Kaushal Silva was run out after scoring 80 off 218 deliveries while attempting to take a single with his captain Angelo Mathews. Silva's knock took more than five-and-a-half hours and included 10 fours.
The dismissal ended a 72-run stand for the fourth wicket with Mathews, who remained unbeaten on 57.
Shah then bowled Dinesh Chandimal (1) and Kithruwan Vithanage (3), and has figures of 3-70.
Dhammika Prasad was on 13.
Pakistan was bowled out for 138 in its first innings on the opening day Thursday.
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