Connolly has decided to rest prop Holmes after he started in each of the Wallabies' eight Tests this season and he will instead now undergo a training program.
Waratahs prop Benn Robinson has taken Holmes' place in the touring squad while new Western Force recruit Drew Mitchell and Brumbies prop Guy Shepherdson rejoin the squad.
Connolly said: "By resting Greg from the Test we will be able to give him an early start on a training program and provide an opportunity for Benn Robinson to compete for a place in the team.
"The front row selections have been very close this year and we've been very conscious of broadening our squad ahead of the World Cup," he added.
Australia squad: Al Baxter, Rodney Blake, Mark Chisholm, Rocky Elsom, Scott Fava, Mark Gerrard, Matt Giteau, George Gregan (captain), Stephen Larkham, Chris Latham, Tai McIsaac, Drew Mitchell, Stirling Mortlock, Wycliff Palu, Jeremy Paul, Clyde Rathbone, Benn Robinson, Mat Rogers, Nathan Sharpe, Brett Sheehan, Cameron Shepherd, Guy Shepherdson, George Smith, Dan Vickerman, Phil Waugh.