Larkham's place will go to utility back Sam Norton-Knight, making his Test debut. Norton-Knight, 23, began his professional career playing on the wing alongside Larkham at the ACT Brumbies but moved to the NSW Waratahs in 2006 to try his luck at fly-half.
Larkham, who has won 95 caps and will join Edinburgh after the Rugby World Cup, will miss his first Test for the Wallabies since 2005.
Australia: Julian Huxley (ACT); Mark Gerrard (ACT), Stirling Mortlock (ACT), Adam Ashley-Cooper (ACT), Drew Mitchell (WF); Sam Norton-Knight (NSW), Matt Giteau (WF); Matt Dunning (NSW), Stephen Moore (QLD), Guy Shepherdson (ACT), Nathan Sharpe (WF), Mark Chisholm (ACT), Rocky Elsom (NSW), Phil Waugh (capt, NSW), Wycliff Palu (NSW)
Replacements: Adam Freier (NSW), Benn Robinson (NSW), Dan Vickerman (NSW), Stephen Hoiles (ACT), George Smith (ACT), George Gregan (ACT), Scott Staniforth (WF)