Michael Clarke's courageous first-innings century in Cape Town has taken on new significance after it was discovered Australia's captain batted for the majority of his innings with a fractured left shoulder.

The fracture was discovered on scans after the captain's return to Australia and the injury has ruled Clarke out of batting for NSW in this weekend's Bupa Sheffield Shield final.

The injury came as the skipper endured a barrage of bouncers from Morne Morkel during the third Test against South Africa in Cape Town.

Quick Single: Relive Clarke's battle with Morkel

Clarke was hit on the forearm, elbow, shoulder and helmet in a fierce spell of short-pitched bowling on the first day, and later on the thumb when the bowler returned with the second new ball. The Australian skipper weathered the storm, and went on to score a brilliant unbeaten 161 hailed by some as the greatest and most courageous knock of his career.

Australia team physiotherapist Alex Kountouris confirmed the break came after being struck by a bouncer.

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

"We expect that this will heal with a period of rest. Michael is therefore unavailable for the Bupa Sheffield Shield final to be played later this week."

Clarke went for a first-ball duck in the second innings when he failed to get enough power into his shot to clear the infield in the chase for quick runs, while he still managed to bowl five overs of left-arm spin in the second innings as the team hunted down the 10 wickets needed for the Test and series win.

Clarke had been worried an injury to his right thumb might keep him out of the Shield final, but he was upbeat about playing on his return to Australia following the 2-1 Test series victory against the world's No.1 team.

Clarke was cleared of any break in his right thumb after the digit was left bloodied and without the nail after being struck by Morkel, but the skipper was intent on returning for NSW.

“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.”

Quick Single: How Australia's stars broke pain barrier

Clarke's physical ailments were highlighted after the Cape Town Test, when team doctor Peter Brukner spoke about the challenge he and Kountouris faced to get the skipper up for the second day's play.

It was revealed after the Test that Clarke's bruises – and now apparent shoulder fracture – prevented him from sleeping after day one. He gave up on the prospect of sleep at approximately 5am on day two, when the medical team helped put him on the path for a stoic innings of 161 not out.

"He was in a lot of pain. He didn't sleep at all that night," Brukner said. "Nothing was serious long term, just short term he was battered and bruised."

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