The batsman made his return to the one-day international side for the first game of the three-match ODI series, which Pakistan won by four wickets, but has now flown home to be with his family.
The PCB confirmed the 36-year-old's departure in a statement on Monday and announced that they would not call up a replacement with only two matches remaining on the tour.
"Younis is returning to Pakistan," the statement read. "And had already left Hambantota for Colombo on Monday afternoon to catch an onward flight to Karachi."
Younis scored 211 runs in the two-match Test series that preceded the ODI matches, including 177 in the opening game, but Sri Lanka went on to win 2-0.
The second ODI takes place on Tuesday, with the final match in Dambulla on Saturday.