The hosts took a 1-0 lead in the two-match series by sealing a remarkable seven-wicket success on Sunday, bowling the tourists out for 180 before reaching the 99 they needed for victory inside 17 overs.
Karunaratne was part of the Sri Lanka side to return from England with a 1-0 series win under their belts in June, although the 26-year-old made just 127 runs in his four innings.
Binura Fernando, an uncapped 19-year-old has also been called up, although it is thought unlikely the left-arm seamer will feature.
The duo replace Nuwan Pradeep and Suranga Lakmal, who are both suffering from ankle problems.
Sri Lanka Cricket also confirmed that Shaminda Eranga has been "nominated" for the Test, subject to fitness.
The clash at the Sinhalese Sports Club begins on Thursday, and will be Mahela Jayawardene's final Test before retirement.