Pakistan, sitting pretty at 285-1 just before lunch on the third day, crashed to 320 all out after the break to leave Sri Lanka a victory target of 171 for a decisive 2-0 lead in the three-match series.
Sri Lanka cruised home by seven wickets with two days to spare, skipper Kumar Sangakkara leading the way with a fluent 46 after opener Malinda Warnapura made 54.
Of the previous five series between the two nations on Sri Lankan soil, Pakistan had won three and drawn two, but the tourists had only themselves to blame for allowing the hosts to re-write history.
Pakistan's meek surrender against the second new ball came after debutant opener Fawad Alam hit a superb 168 and shared a record stand of 200 for the second wicket with skipper Younus Khan (82).
The partnership was Pakistan's highest for the second wicket against Sri Lanka, surpassing the 151 by Mohsin Khan and Majid Khan at Lahore in 1982.
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The 23-year-old Alam batted for more than six hours to amass the highest score