Younus reached the interval on 77, his 29th test fifty, and Misbah on 22 as the experienced pair batted throughout the afternoon session to add 81 runs to the total after Pakistan had lost three early wickets in the morning.
Both batsmen rode their luck with Younus benefiting the most, surviving two lbw decisions and a dropped catch to hit five fours and a six in his 146-ball knock.
Soon after the lunch break, Misbah and Younus survived lbw appeals off the bowling of Sri Lanka captain Angelo Mathews.
Misbah had yet to score when a delivery hit him on the front pad but the Pakistan skipper was given not out. Sri Lanka immediately called for a review which backed up the umpire's call.
In his next over, Mathews jagged one back at Younus, on 20, hitting him on the back foot in front of the wicket but Sri Lanka opted against a review with television replays suggesting the ball would have gone on the hit the middle stump.
Younus then used a review to survive another lbw decision on 59, this time against Dilruwan Perera, whom he had hit for three consecutive fours in a 14-run over to reach his half-century.
Younus got a fourth life upon reaching 68 after he reverse swept Perera to Mahela Jayawardene at slip but the fielder could not hold on to the difficult chance.
Earlier, Sri Lanka paceman Dhammika Prasad struck two early blows as Pakistan reached lunch on 59-3 after Misbah had won the toss and opted to bat.
After a delayed start due to a wet outfield, Pakistan lost both openers to Prasad within the first hour of play, during which they managed just 22 runs.
Prasad, coming in for the injured Suranga Lakmal, troubled Pakistan's batsmen with his pitched up inswingers.
He had Ahmed Shehzad (four) playing onto a delivery with the team's score on four and later trapped Khurram Manzoor leg before for three to reduce Pakistan to 19-2.
Younus joined Azhar Ali in a partnership of 37 before Rangana Herath separated them, removing the latter for 30 with a fine delivery that beat the bat and kissed the off stump.
(Editing by John O'Brien)
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