The decision to withdraw Hooper comes after the 26-year-old felt discomfort in his hamstring during training and as a result David Pocock will lead the side and will move to the number seven slot while Pete Samu takes his number eight position with Ned Hanigan joining the replacements.
Wallabies head coach Michael Cheika said the team management did not want to take a chance with Hooper's fitness.
“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", said Cheika.
“He was really keen to play this weekend but a week off will be a good thing for him to just get it right".
Australia currently are languishing at the bottom of the Rugby Championship table with a solitary win from three games until now.
Australia line-up against Argentina:
Dane Haylett-Petty, Israel Folau, Reece Hodge, Matt Toomua, Marika Koroibete, Kurtley Beale, Will Genia, Pete Samu, David Pocock (C), Lukhan Tui, Izack Rodda, Rory Arnold, Allan Alaalatoa, Tatafu Polota-Nau, Scott Sio
Replacements: Folau Faingaa, Sekope Kepu, Taniela Tupou, Adam Coleman, Ned Hanigan, Nick Phipps, Bernard Foley, Jack Maddocks