The Kent ground had seen Scotland record their first victory over a Test-match country in any format when they won Sunday's one-day tour opener by seven wickets.
But Sri Lanka, using the matches as a warm-up for the Champions Trophy tournament in England and Wales that starts next week, ensured they suffered no fresh embarrassment on Tuesday by cruising to a nine-wicket win.
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Kusal Mendis's unbeaten 74 saw Sri Lanka past a modest target of 166 but it was their bowlers who did most damage to Scotland's hopes of a repeat victory.
Scotland's Kyle Coetzer and Matthew Cross had both scored centuries last weekend. But it was a different story after Sri Lanka won the toss on Tuesday.
Coetzer fell in the third over with just five runs on the board while Cross only managed 27 this time around.
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In reply, Niroshan Dickwell was caught by Matt Watt off Alasdair Evans for 29.
But Sri Lanka enjoyed an otherwise untroubled chase as Upul Tharanga (53 not out) and Mendis saw them to a final total of 170 for one from 22.5 overs.
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