He was his side's main hope after the loss of four wickets, including skipper Mahela Jayawardene, in the opening six overs.
Wicketkeeper Prasanna Jayawardene, who suffered a hairline thumb fracture when struck by a Johnson delivery in the first innings, came out to bat upon Sangakkara's injury retirement.
Sri Lanka, trailing by 304 runs on the first innings, were facing a heavy defeat inside three days of the Boxing Day Test after losing the Hobart series opener by 137 runs last week.