The tourists, who resumed their second innings at 127-7 chasing a target of 271, were shot out for 165 before lunch on the fifth day at the Sinhalese Sports Club.
Last man Junaid Khan was unable to bat due to injury.
Left-arm spinner Rangana Herath, who claimed nine wickets in the first innings, was once against the chief destroyer with five for 57 in the second.
Sri Lanka President Mahinda Rajapakse was among the 4,000 home fans to bid goodbye to Jayawardene, who ended his 17-year Test career with this series.
The 37-year-old will continue to play one-day matches till next year's World Cup in Australia and New Zealand.
Sri Lanka won the first Test in Galle by seven wickets.
The two teams will now clash in three one-day internationals starting on August 23.
Brief scores:
Sri Lanka 320 and 282; Pakistan 332 and 165
COMMENTS (3)
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Whenever our media depict stories like(Pak team in winning mood) then our team make sure just the opposite-poor media managers and others as well.
Just SL ? I guess it was perfect farewell given from Pakistan as well.They were throwing their wickets on average bowling.
Fruits of fraudulent leadership of Najam Sethi. Pakistan cricket in tartars