Beale, who has been on the bench in recent matches, was left out of the matchday 23 altogether after the ARU confirmed it had launched a probe into the incident which occurred when the Wallabies were in transit from South Africa to Argentina.
McKenzie put a split of six forwards and two backs on the bench, rationalising in a statement on Thursday that the Wallabies needed all the muscle at their disposal for Saturday's match in Mendoza.
In two changes to the starting side, former captain James Horwill replaces concussed lock Rob Simmons, while Scott Higginbotham comes in as expected for the injured Ben McCalman at number eight.
Australia: 15-Israel Folau, 14-Adam Ashley-Cooper, 13-Tevita Kuridrani, 12-Matt Toomua, 11-Joe Tomane, 10-Bernard Foley, 9-Nick Phipps, 8-Scott Higginbotham, 7-Michael Hooper (captain), 6-Scott Fardy, 5-James Horwill, 4-Sam Carter, 3-Sekope Kepu, 2-Saia Faingaa, 1-James Slipper
Replacements: 16-Josh Mann-Rea, 17-Benn Robinson, 18-Ben Alexander, 19-Will Skelton, 20-Jake Schatz, 21-Matt Hodgson, 22-Nic White, 23-Rob Horne