Pakistan started their second innings disastrously; openers Khurram Manzoor, Ahmed Shehzad and Mohammad Hafeez perished either side of the lunch session with the scoreboard reading a precarious 19 for three.
Younus (62 off 142balls) and Misbah (53 off 119) added 113 runs in their unbroken fourth wicket association.
The hosts finished the day at 132 for three, 91 runs behind Sri Lanka's total, with seven wickets in hand and two more days to play.
Earlier, Sri Lanka finished their first innings at 388, a lead of 223 runs after Pakistan’s paltry 165 runs first innings effort.
The tourists lost their last seven wickets for the addition of 70 runs only as Junaid Khan, Rahat Ali and Saeed Ajmal combined well on the third day.
Junaid captured three while Ali and Ajmal took two wickets each.
Mahela Jayawardene the former Sri Lanka captain top-scored with 129 runs, he fell to Ajmal after his outstanding knock.
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