Australia captain Michael Clarke batted with a broken shoulder on the recent tour of South Africa and has been advised to rest, ruling him out of the domestic first class final later this week, Cricket Australia said on Monday.

Clarke, who led his side to a 2-1 Test series victory over South Africa, was struck on the left shoulder during the third Test in Cape Town earlier this month, and still went on to make 161 not out in the tourists' first innings.

"We have since done a series of scans that have demonstrated a fracture near his shoulder joint," Australian team physiotherapist Alex Kountouris said in a statement. "We expect that this will heal with a period of rest."

Clarke's New South Wales team will play Western Australia in the domestic Sheffield Shield final in Canberra from March 21-25.

Clarke, who was also struck in the arm, thumb, elbow and helmet in the Cape Town match, was due a long break away from the game anyway as he was not in Australia's squad for the ongoing World Twenty20 tournament in Bangladesh. Clarke was, however, cleared of any serious injury to his thumb, which was left bloodied and without the nail after being struck during another Morkel stint.