The virus outbreak could force England to change the team for the Test which had been announced on Tuesday.
Security issues have meant Pakistan have had to play most of their home Tests of the last two decades on neutral grounds, usually the United Arab Emirates.
Shafique hit the winning runs in the final session of play on day five to take a 1-0 lead in the two-match series.
The Galle International Stadium will host its fourth straight Test in the past few weeks after the two Australia matches and the ongoing Pakistan opener.
All-rounder Dhananjaya de Silva, pacer Asitha Fernando and spinner Jeffrey Vandersay are all named in the squad and are in contention to return to Sri Lanka's XI.
Australia vs Pakistan second Test: Pat Cummins strikes before lunch as Abdullah Shafique falls for 96
Cummins struck eight minutes before lunch to end an epic third-wicket stand of 228 between Shafique and Pakistan captain Babar with the score on 249.
Pakistan came back in the last hour when Faheem Ashraf (1-20) found the outside edge of Warner’s bat off a delivery that moved a fraction away from the left-hander.