Jayawardene, 36, will miss two Twenty20 games and five one-dayers to be played from December 11-27, but was expected to be available for the three Test matches that start on December 31.
"Mahela was not considered for the limited-overs part of the tour as he had requested leave on personal grounds," Sri Lanka Cricket's media manager Rajith Fernando said. The Cricinfo website reported that Jayawardene's wife was expecting their first child in December.
Jayawardene is one of 10 batsmen and only the third Sri Lankan after Sanath Jayasuriya and Kumar Sangakkara to score more than 10,000 runs in one-day internationals. The stylish right-hander has made 11,401 runs in 407 one-dayers with 16 centuries and 1,135 runs in 49 Twenty20 internationals.
Left-hander Kithuruwan Vithanage, 22, who has played two Tests but is yet to make his one-day debut, replaced Jayawardene in the limited-overs squad. Sri Lanka named their one-day and Twenty20 squads for the tour, but will announce their Test team later.
Sri Lanka's one-day squad: Angelo Mathews (capt), Tillakaratne Dilshan, Kusal Perera, Dimuth Karunaratne, Kumar Sangakkara, Dinesh Chandimal, Lahiru Thirimanne, Ashan Priyanjan, Kithuruwan Vithanage, Thisara Perera, Nuwan Kulasekara, Lasith Malinga, Suranga Lakmal, Sachithra Senanayake, Rangana Herath, Seekkuge Prasanna.
Sri Lanka's Twenty20 squad: Dinesh Chandimal (capt), Lasith Malinga, Tillakaratne Dilshan, Kusal Perera, Kumar Sangakkara, Angelo Mathews, Lahiru Thirimanne, Kithuruwan Vithanage, Thisara Perera, Nuwan Kulasekara, Seekkuge Prasanna, Suranga Lakmal, Sachithra Senanayake, Ajantha Mendis, Ramith Rambukwella.