Sri Lanka won the series 1-0 after a crushing 10-wicket victory in the first game was followed by washouts in Colombo on Friday and Sunday.
The prospects of play had looked good on Sunday morning after a largely dry weekend but a torrential tropical storm minutes before the scheduled toss left large swathes of a muddy outfield under water.
"It was obviously disappointing as we were here to play cricket and there is nothing worse for a cricketer than staying in the dressing room," Atapattu said.
"Whether we like it or not, however, we will just have to be satisfied with our victory in Dambulla -- we played really well there and deserve the trophy for that.
"The 1-0 win will be a good morale booster before the forthcoming Test series."
England's one-day defeat was their first since Michael Vaughan took over the captaincy from Nasser Hussain after the World Cup.
"We didn't play well in the opening match and we were looking forward to testing our young players in tough conditions here in Colombo," Vaughan said.
"It was very disappointing that we didn't get a chance to come back in the series and that the players didn't get useful exposure against a very good team," he added.
England are due to play a three-day match against a Sri Lanka Board President's XI starting on Wednesday before the first Test in Galle begins on Dec 2.
"We now have to hope that the weather is good for the next week and that we get in a good week's preparation before the first Test," said Vaughan.