Beale was injured in the Melbourne Rebels' 66-24 loss to the Wellington Hurricanes on Saturday and Wallabies coach Robbie Deans had said earlier on Monday he expected he would not be available for the June tests against Scotland and Wales.
The fullback-turned-flyhalf had been earlier included in the 39-man Wallabies squad for the tests.
"Kurtley Beale had surgery today (Monday) to clean out floating cartilage from his left shoulder joint," the Rebels said in a statement.
"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."
Deans, who had spoken to media in Sydney before the Wallabies entered a training camp, said Australia captain James Horwill had torn his hamstring.
The towering lock sustained the injury early in the second half of the Queensland Reds' 13-12 win over the ACT Brumbies in a Super Rugby match in Canberra on Saturday.
Despite the injury, the skipper had joined up with the Australia squad and coaching staff in Sydney and underwent a scan on Monday.
The coach said Horwill's injury was not as bad as he had earlier feared.
"James, we are presuming, is out for the whole of June but it is not as bad as it first looked. It looked pretty sinister at the time," Deans said.
Horwill's absence will force the Wallabies to name a new captain for the match against Scotland on June 5 in Newcastle before the first of three tests against Six Nations champions Wales on successive weekends from June 9.
Scrumhalf Will Genia and openside flanker David Pocock are the leading candidates to skipper the Tri-Nations champions in the absence of Horwill.
With a final round of Super Rugby games to be played before the international break, Deans will name his team on Sunday for the Scotland test on June 5.