Johnson will resume the third day with Nathan Lyon yet to score.
Clarke reached his batting milestone when he got to 56 shortly before lunch. His total for the year is now 1,595, eclipsing recently retired Ricky Ponting's previous record of 1,544 in 2005.
After resuming on the overnight score of 150-3, Clarke made a watchful start before loosening his strokes against a tame Sri Lankan attack. He timed 14 boundaries, showing little sign of the hamstring strain sustained in the first test at Hobart.
One of Clarke's fours came courtesy of an error when Eranga fielded a straight drive off his own delivery only to beat Kumar Sangakkara behind the wicket with a return that carried to the boundary.
