The 30-year-old Pocock also shifts from number eight to openside flanker, with Pete Samu coming into the starting lineup at the back of the scrum for Saturday's clash. Ned Hanigan moves onto the bench to cover the loose forwards.
Hooper suffered a hamstring injury during the test series against Ireland in June and did not play again until the Rugby Championship started last month.
"He felt his hamstring a bit at training yesterday afternoon and with his recent history, we just thought it was best not to push it," coach Michael Cheika said in a statement on Friday.
"He was really keen to play this weekend but a week off will be a good thing for him to just get it right."
Revised team: 15-Dane Haylett-Petty, 14-Israel Folau, 13-Reece Hodge, 12-Matt Toomua, 11-Marika Koroibete, 10-Kurtley Beale, 9-Will Genia, 8-Pete Samu, 7-David Pocock (captain), 6-Lukhan Tui, 5-Izack Rodda, 4-Rory Arnold, 3-Allan Alaalatoa, 2-Tatafu Polota-Nau, 1-Scott Sio.
Replacements: 16-Folau Faingaa, 17-Sekope Kepu, 18-Taniela Tupou, 19-Adam Coleman, 20-Ned Hanigan, 21-Nick Phipps, 22-Bernard Foley, 23-Jack Maddocks.
(Reporting by Greg Stutchbury in Wellington; Editing by Ian Ransom)
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