Beale, who has successfully switched to fly half from full back for the Melbourne Rebels in this season's Super Rugby season, is likely to be out for at least a month.
"Kurtley Beale had surgery today to clean out floating cartilage from his left shoulder joint," the Rebels said in a statement earlier today.
"Beale will be closely monitored over the coming days, but the initial assessment is that he will be unavailable for the next three to four weeks.
The injury crisis means Cooper has suddenly come into the reckoning for a starting spot after he was named in the Wallabies training squad for the forthcoming Tests.
The Qantas Wallabies train on squad is: Ben Alexander, Adam Ashley-Cooper, Berrick Barnes, Quade Cooper, Dave Dennis, Kane Douglas, Anthony Faingaa, Saia Faingaa, Bernard Foley, Will Genia, Michael Harris, Scott Higginbotham, Michael Hooper, Rob Horne, Digby Ioane, Sekope Kepu, Salesi Ma'afu, Pat McCabe, Ben McCalman, Jesse Mogg, Stephen Moore, Luke Morahan, Cadeyrn Neville, Dan Palmer, Wycliffe Palu, Nick Phipps, David Pocock, Tatafu Polata Nau, Hugh Pyle, Benn Robinson, Nathan Sharpe, Dominic Shipperley, Rob Simmons, James Slipper, Sitaleki Timani, Joseph Tomane, Cooper Vuna, Nic White.