The 22-year-old had originally been named in the starting lineup by coach Robbie Dean, but he has been unable to recover from the complaint.
As a result, Adam Ashley-Cooper will switch to full-back with Anthony Fainga'a due to start at outside centre.
"We always anticipated it would be unlikely that Kurtley would be ready, but we wanted to give him every opportunity to make it," said Dean. "Unfortunately time has run out.
"It was important for the clarity of the preparation, both for the team and for Kurtley, that we made the decision today."
Beale is expected to be fit should Australia advance to the final.