Australia captain Michael Clarke's courageous century in the decisive Third Test against South Africa took on added significance today when it was revealed he played with a fractured shoulder.

Clarke weathered a fearsome barrage of bouncers on the first day of the Cape Town Test this month, being hit on the forearm, elbow, shoulder and helmet in a fiery spell of short-pitched bowling by Morne Morkel.

He went on to a make a pivotal 161 not out, hailed by many as the best knock of his career, to help his team deliver a 2-1 series victory.

The results of scans released today showed he played with a fractured left shoulder that has ruled him out of the domestic Sheffield Shield final this weekend, where he had hoped to play for New South Wales against Western Australia.

"Michael Clarke was injured as a result of being struck on the left shoulder during the third Test against South Africa in Cape Town," said Australian team physiotherapist Alex Kountouris.

"We have since done a series of scans that have demonstrated a fracture near his shoulder joint.

"We expect that this will heal with a period of rest."

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.

Despite the battering he took in Cape Town, Clarke had been keen to play for NSW in the Shield tournament.

"I've got a few injuries from that second last innings, so I'll spend some time recovering and trying to get my body right and hopefully I'll be able to play in the Shield final for NSW," Clarke said upon his return from South Africa.

"But I'm in good hands. I've got a good physio here in Sydney and I think I'll be fine. I'll just take some time for the body to heal and the mind as well.

"It's been a busy six months and mentally that's as challenging as physically, so I'm looking forward to being home with family and friends and enjoying the simple things."

It was revealed after the Test that the battering Clarke took prevented him from sleeping after day one. He went to stumps that day unbeaten on 92 and returned to complete a stoic innings of 161.

Australia are not due to play another Test series until they travel to the United Arab Emirates to face Pakistan in October.