It was yet more misery, too, for Shane Watson, who missed out on his third Test century and his first hundred since October 2010 when he fell for a Sri Lankan sucker punch on 83.
At the close on the second day Australia were 440 for eight, with paceman Mitchell Johnson on 73 and Nathan Lyon yet to score. Australia had extended their lead over the tourists to 284 runs with two wickets intact.
Clarke went into the Melbourne Test needing 56 runs to break Ponting's national record and has now amassed 1,595 runs at 106.33 in Australia's final Test of the year. Clarke was finally caught by rival skipper Mahela Jayawardene in the slips off Shaminda Eranga after 251 minutes at the crease.
Clarke, who was in doubt ahead of the game with a hamstring injury, has also scored a triple century and three double centuries in an extraordinary year. But it was not a chanceless innings, with Clarke having a let-off in Rangana Herath's 17th over when substitute 'keeper Kumar Sangakkara missed a tough stumping chance on 54. He was also dropped by Tillakaratne Dilshan on five late on Wednesday's first day.
Clarke put on 194 runs for the fourth wicket with Watson, who soon followed his skipper back to the dressing room after again failing to convert a half-century into a ton.
Watson suffered an injury to his left calf while bowling in Sri Lanka's first innings and may not bowl in their second innings, it was announced late Thursday.