After winning the toss and electing to bat, the tourists got off to a slow start and lost wickets at regular intervals on a slugging pitch.
Jos Buttler hit 21 but England slipped to 60-6 in the 11th over as the middle-order succumbed to the home team's spinners.
It took a brisk knock from Sam Curran, who struck 58 off 48 balls, to take the visitors to a total of 128-9 in their 20 overs.
While Sri Lanka's spinners caused havoc at the start and in the middle of the innings, seamer Dushmantha Chameera cleaned up the lower-order to finish with career-best figures of 5-24 in four overs.
The home side's run-chase followed the same pattern as first innings with wickets falling throughout and failing to stitch any meaningful partnerships together.
Jacob Bethell had quite the day out with the ball as the left-arm spinner grabbed a remarkable 4-11 in 3.3 overs as the hosts were bowled out for just 112 in the final over.
England will take plenty of confidence into the T20 World Cup after winning all three matches in the shortest in the co-hosting country.
England head coach Brendon McCullum insists Harry Brook is a "strong leader" and the right man lead the white-ball teams despite plenty of off-field controversies in recent months.
Sri Lanka have confirmed their 15-man squad for the ICC Men's T20 World Cup 2026, backing experience at the top while making decisive calls in the middle order ahead of the tournament's start this weekend.
Tom Banton's composed unbeaten half-century and a ferocious Harry Brook cameo steered England to a six-wicket victory over Sri Lanka in a rain-reduced second T20 international, sealing the series 2-0 in Pallekele.
England got their T20 series against Sri Lanka off to a perfect start as Sam Curran claimed a stunning hat-trick to help secure an 11-run win on the DLS method in Pallekele.
