The third match in Kandy, which England won by seven wickets on Wednesday, was delayed by six hours due to persistent rain and reduced to 21-overs each side.
"After hosting England, Sri Lanka spend the rest of the 18-19 season touring New Zealand, Australia and South Africa," the ECB said in a statement.
"They play their first match in New Zealand on Dec. 8, which left very little wriggle room given our final test in Sri Lanka finishes on Nov. 29.
"The Future Tours Programme is congested ... so there are unfortunately a number of tours that have to take place outside prime match-staging periods."
Eoin Morgan's side will play further one-day matches against Sri Lanka on Saturday and Tuesday, before a Twenty20 game in Colombo on Oct. 27.
England will then face the hosts in a three-test series, which begins in Galle on Nov. 6.
(Reporting by Hardik Vyas in Bengaluru)
