The controversial play-maker has endured a torrid year in which he has been plagued by off-field problems.
He was recalled by Robbie Deans and played in every Test against the British & Irish Lions as the tourist sealed a 2-1 series victory.
But Beale has been carrying a shoulder injury and new Australia coach Ewen McKenzie has instructed him to get the problem fixed.
"It's pretty simple, Kurtley's had a shoulder injury for more than a year now," said McKenzie.
"As a result, he's missed some football. I've been talking to the medical side of the business and there's a lot of guys carrying damage.
"When you're carrying a shoulder injury for a long period of time it has an impact on your game. We felt the best thing for him was to get it fixed.
"By doing it now it allows him the opportunity of a pre-season and then he can play a lot of Super Rugby and be 100 percent to play Test football next year.
The 39-times capped Wallaby is expected to sign with NSW Waratahs in the coming weeks, drawing the curtain on two controversial years with Melbourne Rebels.
Beale has constantly courted headlines for the wrong reasons and March he was suspended following a drunken assault on Rebels teammates Gareth Delve and Cooper Vuna.
Another indiscretion saw Beale indefinitely suspended by the Rebels and the 24-year-old returned to Syndey for counselling for alcohol abuse.
During the Lions series Beale was photographed in a fast food restaurant in the early hours of the morning during the week of the second Test, along with James O'Connor.