He and Dinesh Chandimal (39 not out) then added 67 runs to stretch the lead before bad light forced early stumps with Sri Lanka in firm control of the series-deciding contest.
Having claimed the last Pakistani wicket in the morning to bowl out the visitors for 215, Sri Lanka wobbled early in their second innings with Rahat Ali troubling their batsmen in a brilliant display of swing bowling.
The left-arm paceman first pegged back the off stump of Dimuth Karunaratne, a first innings centurion, then repeated the feat against Lahiru Thirimanne to wreck the top order.
His new ball partner Ehsan Adil got in on the act when he coaxed an edge from Kaushal Silva to claim the other Sri Lanka wicket to fall in a stop-start morning session interrupted by several rain delays.
Upul Tharanga (48) looked the most fluent of the Sri Lankan batsmen, hitting six boundaries in his nearly run-a-ball knock as he counter-attacked with aggression.
The southpaw, however, fell short of his fifty with Azhar Ali taking a smart bat-pad catch at forward short leg off Yasir Shah.
Back in the test squad after nearly eight years, Mubarak joined his captain in rebuilding the innings but was dismissed for 35 by Shah, who claimed his 24th wicket in the series.
Chandimal ensured Sri Lanka kept piling on runs, hitting five boundaries in his innings.
Earlier, Sarfraz Ahmed remained not out after a defiant 78 as Pakistan conceded a 63-run first innings deficit.
Spinner Tharindu Kaushal deceived the scoreless Imran Khan with a straighter delivery that hit the off stump, leaving Sarfraz stranded as Pakistan could only add six runs to their overnight 209-9.
(Reporting by Amlan Chakraborty in New Delhi; Editing by John O'Brien/Sudipto Ganguly)
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