The 37-year-old, who has injured his patella tendon, is also a doubt for the third test.
Wicketkeeper Prasanna Jayawardene returned to full training this week, but was also not considered for selection as Sri Lanka, who lead the three-match series 1-0 after a 50-run victory in Galle, named an unchanged squad.
The only selection dilemma is the form of opener Malinda Warnapura, who has scored just 12 runs in his last four innings.
Sri Lanka skipper Kumar Sangakkara called for improvement from his batsmen.
"We had a great final day in Galle but we all know that we were not at our best during the first three days and we have to improve," Sangakkara told Reuters.
"The batsmen in particular have been working really hard this week," he added.
"We need to be more patient, be much tighter with our techniques and work through tough phases against a decent bowling attack."
Pakistan captain Younis Khan put the first test defeat down to the pressure on his young players as the team collapsed from 71 for two to 117 all out in the second innings.
"We have youngsters in the team and I think they will learn from their mistakes," he said.
"If we play to our potential in the next two tests we may square the series or win it."
Former skipper Shoaib Malik, who bats at number six, could find his place under scrutiny. He last scored a century in March 2006.
Young all-rounder Fawad Alam, 23, could be a possible replacement after an impressive 83 not out in a warm-up game before the Galle Test.
Sri Lanka squad: Kumar Sangakkara (captain), Malinda Warnapura, Tharanga Paranavitana, Mahela Jayawardene, Thilan Samaraweera, Tillakaratne Dilshan, Angelo Mathews, Chamara Kapugedera, Rangana Herath, Ajantha Mendis, Thilan Thushara, Nuwan Kulasekara, Dhammika Prasad, Kaushal Silva, Suranga Lakmal.
Pakistan squad: Younis Khan (captain), Salman Butt, Khurram Manzoor, Mohammad Yousuf, Misbah-ul-Haq, Shoaib Malik, Kamran Akmal, Umar Gul, Saeed Ajmal, Mohammad Aamer, Danish Kaneria, Abdul Razzaq, Abdur Rauf, Fawad Alam, Faisal Iqbal.
