The 35-year-old, back in the Wallabies squad for the first time in three years, hobbled off during a low-level domestic fixture at the weekend with scans confirming the serious injury.
"Kurtley Beale will undergo surgery for a ruptured Achilles today and we wish him all the best for a successful recovery," the Wallabies said on Instagram.
A timeframe for Beale's return was not given, with some reports suggesting the injury could be career-ending for a player who has been capped 95 times.
In a double blow ahead of the first of two Tests against Wales in Sydney on July 6, centre David Feliuai was also ruled out, due to "personal reasons".
Beale only returned to professional rugby midway through the Super Rugby season with Western Force after being sidelined for more than a year fighting sexual assault charges.
Beale was cleared in February of the allegations, which he always denied, and said last week he was relishing the chance to play for Australia again.
Wallabies teammate Andrew Kellaway called the injury a "massive shame".
"I grew up watching him and eventually playing with someone who I now consider a close mate. It sucks to see after he was right back on the brink of where he used to be," Kellaway told reporters.
Flanker Fraser McReight added: "It's super sad and everyone is feeling for Kurtley.
"No one ever wants to hear someone doing their Achilles or a major injury like that, so everyone is feeling for him."
The Wallabies, who have slumped to ninth in the rankings, are looking to bounce back against Wales in their first games under new coach Joe Schmidt, who replaced Eddie Jones.
