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