New South Wales Waratahs prop Tom Robertson will take Alaalatoa's spot on the bench.
"Robertson has starred for the Waratahs in ... Super Rugby this season, forming a strong front row partnership with fellow Wallaby Sekope Kepu," the team said in a statement.
Alaalatoa's injury follows another reshuffle after hooker Jordan Uelese was ruled out with a season-ending knee injury earlier this week.
Debutant Brandon Paenga-Amosa will start in the number two jersey alongside experienced props Scott Sio and Kepu.
Six Nations champions Ireland are seeking to extend their 12-match winning streak against Michael Cheika's Wallabies and grab their first test and series win in Australia since 1979.
(Reporting by Ian Ransom; Editing by Greg Stutchbury)
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