Beale, who announced a lucrative deal with English Premiership side Wasps last week, injured his patella after falling awkwardly in the opening minute of the Waratahs' win over the Bulls in Sydney on Saturday.
"The procedure went well with a good fixation of the patella tendon back onto the patella bone," the Waratahs said in a media release.
"Beale will remain sidelined for four to six months and will spend the next six weeks in a range of motion braces."
The injury ends Beale's final season with the Waratahs prematurely, while ruling him out of the June internationals against England and at least part of the southern hemisphere Rugby Championship which starts in August.
In the worst case, the versatile back could also miss the start of his debut season with Wasps and struggle to be fit for the Wallabies' season-ending tour of the northern hemisphere which starts against Wales in Cardiff on Nov. 5.
(Reporting by Ian Ransom; Editing by Sudipto Ganguly)