Beale, who is sure to face the Lions next year, is one of three changes, one positional, for the third and final Test in Sydney on Saturday.
"It has been frustrating for Kurtley, and he's obviously had some off-field challenges to deal with as well," said Wallabies coach Robbie Deans.
"But it was important for all concerned that he had full confidence in his shoulder before we looked at re-introducing him to the Test arena."
Elsewhere, Adam Ashley-Cooper moves from full-back to the right wing in place of Cooper Vuna, who escaped punishment for his mid-air tackle on 2009 Lion Leigh Halfpenny. Waratahs lock Sitaleki Timani replaces Rob Simmons in the only other change to the starting XV.
Deans expects a fierce backlash from Wales following their heartbreak in Melbourne last week, where Wallaby replacement Mike Harris slotted an injury time penalty to snatch the win.
"Wales are a very good side," added Deans.
"They give you nothing and they take their scoring chances. They showed that in the Six Nations, and they showed it again last weekend,.
"Both games in the series to date have been very close, there's no reason to suggest that Saturday afternoon will be any different."
Australia team to face Wales: Kurtley Beale; Adam Ashley-Cooper, Rob Horne, Pat McCabe, Digby Ioane; Berrick Barnes, Will Genia; Benn Robinson, Tatafu Polota Nau, Sekope Kepu, Sitaleki Timani, Nathan Sharp, Scott Higginbotham, David Pocock (capt), Wycliff Palu.
Replacements: Stephen Moore, Ben Alexander, Dave Dennis, Michael Hooper, Rob Simmons, Nic White, Anthony Faingaa.