Earlier, Shanaka led another starring role for Sri Lanka's middle-order after England won the toss and made the home side bat at the Pallekele stadium.
The hard hitting Shanaka did not disappoint on this occasion figuring in two half-century stands with Dhananjaya de Silva (17) and Thisara Perera (44) before being run out for an accomplished innings of 66 scored at a run a ball inclusive of five sixes and four fours.
England have now won their past nine one-day series of two or more matches following a 2-1 defeat by India in January 2017, having lost the sole ODI against Scotland a year ago.
Joe Root (32 n.o.) and Eoin Morgan (31 n.o.) put together a partnership of 56 and made certain that their side stayed ahead of the required par score as the dark clouds gathered.
But England were ahead of the rate on 132-2 from 27 overs when play was suspended at 11:15 BST in Pallekele.
Moeen Ali was England's most effective bowler, taking 2/55 as the tourists used a mixture of spin and pace to maintain pressure.
Sri Lanka could have captured the wicket of Root when he was on 22 but for a careless technical mistake on their part in the 23rd over bowled by Dhananjaya de Silva.More news: Canada Post rotating strikes begin in four cities
Sri Lanka captain Dinesh Chandimal felt it could have been a different story if Root had been dismissed when he was caught sweeping, but got a reprieve as umpire Lyndon Hannibal spotted they did not have enough men in the circle.
The fifth and final one-dayer will be played in Colombo on Tuesday. Had he not attempted a suicidal single just as he was starting to ramp up the big hitting in the death overs, Sri Lanka might have managed a score closer to 300.
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The 27-year-old hit five sixes and four boundaries in his run-a-ball innings before getting run out.
Except that Plunkett is now a player on the England cricket tour.
"If we had not made a mistake of having five fielders outside the circle and got Root's wicket it would have been a close game". "We can take the positives and are looking forward to the next game".
Thisara and Akila Dananjaya produced a late flurry as Sri Lanka took 83 off the last 10 overs to post a challenging target, England falling short of their usual high standards in the field.