Vaas took six wickets in the first two Tests as well making his maiden Test century in the opener in Colombo as the hosts opened up an unassailable 2-0 lead in the series.
But he has been granted dispensation to miss the third and final game so he can resume county duties with Middlesex.
Sri Lanka Cricket secretary Kanangan Mathivanan said: "Chaminda Vaas has been released to play county cricket and we have included another left-arm fast bowler Sujeewa Silva in the squad for the third Test in Kandy."
"Nothing has been finalised with regards to the final team. It is very likely that the final line-up will be decided the day before the game or on the morning of the match."