Younis fell for 77 in a slow opening session which saw Pakistan reach lunch on 189 for four, still 34 runs shy of Sri Lanka's first innings total.
Mishbah-ul-Haq continued to chip away at that deficit, moving to 74 before the break, while Asad Shafiq was unbeaten on 18 at the other end.
Pakistan had resumed on 132 for three, with both Younis and Misbah having passed the half-century mark the previous evening.
The pace was plodding, Misbah failing to score a single run in the opening hour's play as he blocked, blocked and blocked again, and the fall of Younis was about the only moment of drama in the entire session.
It came in the 11th over of the day as the result of a misjudgement from the batsman, tempted by a short delivery from Suranga Lakman.
He thought he could cut it but only succeeded in edging behind into the grateful gloves of Prasanna Jayawardene.
Misbah suddenly came to life after the drinks break, scoring seven off a single Lakman over, but it was a rare explosion with Pakistan and their captain all too aware that they cannot afford to give any more wickets away.