Younus, who resumed at 306, played on to Sri Lanka's Dilhara Fernando in the ninth over of the final day, disappointing the still-sparse crowd at National Stadium who had hoped to see Brian Lara's record 400 broken.
The 31-year-old also fell 24 short of Hanif Mohammad's Pakistani record of 337 as the home team reached 662-6 by lunch, a lead of 18 runs over Sri Lanka's 644-7 declared.
Wicketkeeper-batsman Kamran Akmal, approaching his century, was unbeaten on 89 at the break.
The other not-out batsman was Yasir Arafat on 17 as the match headed for a draw.
Younus, who came to the crease on Sunday for his first innings as Pakistan captain, batted for a marathon 12 hours and 48 minutes, facing 568 balls and hitting 27 boundaries and four sixes.
His triple ton eclipsed Sri Lankan skipper Mahela Jayawardene's 240, part of a record 437 fourth-wicket stand with Thilan Samaraweera (231), but did not trouble West Indian Lara's record set against England in 2004.
Hanif's national ma