Only nine of the 15 players who represented the country in the World Cup have been named in the squad for the series starting on May 18.
Veterans Kumar Sangakkara, Muttiah Muralitharan and Chaminda Vaas were released by governing body Sri Lanka Cricket to play county cricket in England.
Russel Arnold has retired from international cricket while seamer Nuwan Kulasekara, who played one game in the World Cup, was left out along with Atapattu.
Asantha de Mel, Sri Lanka's chairman of selectors, said that they decided to drop Atapattu as they wanted to groom young players.
"We just thought of taking this opportunity to take a look at a few young players. Marvan will be considered in the future, but for this series we thought of going with a couple of young guys," de Mel said.
Uncapped opening batsman Malintha Warnapura (27) has been named in the squad after his excellent form with the "A" team, along with Ishara Amarasinghe (28), another uncapped player.
"Malintha deserves the break. He's done exceptionally well with the 'A' team and his choice was automatic. Ishara bowls at a good pace and he's got the talent and we want to see how he goes," de Mel added.
"He's someone like Lasith Malinga, unusual action and troubles batsmen often."
Prasanna Jayawardene, who keeps wicket in Tests for Sri Lanka, has been named wicketkeeper in the absence of Sangakkara.
Leg-spinner Kaushal Lokuarachchi and middle order batsman Chamara Kapugedara complete the squad.
Sri Lanka squad: Mahela Jayawardene (Captain) Sanath Jayasuriya, Upul Tharanga, Chamara Silva, T.M. Dilshan, Farveez Maharoof, Dilhara Fernando, Malinga Bandara, Lasith Malinga, Malintha Warnapura, Prasanna Jayawardene, Ruchira Perera, Ishara Amarasinghe, Kaushal Lokuarachchi, Chamara Kapugedara.