Younus top-scored with 76 and Misbah-ul Haq hit an unbeaten 73 to steer Pakistan to 279-8 after they won the toss and elected to bat in the day-night match at the Premadasa stadium.
Teenage paceman Mohammad Aamer grabbed 4-28 and Rana Naved took 4-44 as Pakistan bowled out Sri Lanka for 147 in the 35th over to record their second successive win after Friday's 146-run success.
Sri Lanka, however, clinched the one-day series 3-2, after winning the Test series 2-0.
The rivals, who contested the World Twenty20 final in England in June when Pakistan won the title, will play a T20 international here Wednesday in the last match of the tour.
The half-centuries from Younus and Misbah helped Pakistan recover from the first-ball dismissal of Kamran Akmal, who was given out leg-before off Nuwan Kulasekara despite getting an edge on the bat.
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Younus put on 69 for the third wicket with veteran Mohammad Yousuf (43) and 83 for the fourth, with Misbah before being bowled by seamer Dammika