Australian captain Michael Clarke battled on to his pivotal century in Cape Town with a broken shoulder, scans have revealed.

Michael Clarke’s pivotal century in the third Test against South Africa will go down as one of the most courageous in history, after scans revealed the Australian skipper batted most of his innings with a fractured shoulder.

Before the summer’s Ashes series, Clarke was struggling to shake a perception he wasn’t as tough a presence on the field as his forebears.

However, Clarke’s testy, expletive-laden exchange with England’s James Anderson in Brisbane, and now his stoic innings in Cape Town have helped the skipper well and truly transform from pretty boy to warrior.

The ball that caused the broken shoulder was a brutal bouncer from Proteas fast bowler Morne Morkel that deflected up and smashed Clarke on the side of his head, under his helmet.

At the time, the 32-year-old was hailed for his bravery, but now two weeks on the full extent of what he put himself through in Cape Town has finally become clear.

In addition to his fractured shoulder, Australian medicos were worried about the effects of Clarke’s head-knock, with a visible lump left on his neck.

And from the same vicious spell of Morkel bowling, Clarke also had his nail ripped off his thumb, in what was suspected at the time to be another broken-bone injury.

Clarke was 13 not out when the body-blow barrage started. He finished day one on 92 not out.

Unable to sleep a wink that night due to the pain, Clarke returned the next morning and when Australia declared in a match-winning position at 7(dec)-494 at the end of day two, Clarke was unbeaten on 161.

With a series against the world No.1 Test side on the line, Clarke’s innings was reminiscent of Steve Waugh’s gutsy century at The Oval in 2001 nursing a torn calf, South African captain Graeme Smith returning to bat with a broken hand against Australia in 2009 and Rick McCosker batting with a broken jaw in the Centenary Test in 1977.

Clarke had arrived at NSW cricket headquarters for scans on Monday to see whether he could be passed fit to play for the Blues in Friday’s Sheffield Shield final against Western Australia in Canberra.

But the Blues will have go to battle without him after a fracture near the joint of his shoulder was confirmed.

“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 physiotherapist Alex Kountouris.

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

NSW coach Trevor Bayliss said the silver lining of losing Clarke was that the Blues don’t have to drop a batsman who has powered them into the final.

“We’ve got to where we are without him for most of the season so it’s a good reward for the batters in the team who have done the job all year,” Bayliss said.

Bayliss said the bigger loss will be fast bowler Doug Bollinger, who has been called up to Australia’s World Twenty20 squad as an injury replacement for Mitchell Johnson.

However, NSW do welcome back allrounder Moises Henriques from international duty.