Hooker Dave Porecki will lead the Wallabies in the Pool C match in his absence, while Richie Arnold will take his place in the second row and Matt Philip comes in as cover for the locks on the bench.
Skelton's injury is a second blow for Australia this week as they prepare for a match at Stade Geoffroy-Guichard which could all but earn them a place in the quarter-finals.
Tighthead prop Taniela Tupou will miss the match after sustaining a hamstring strain also described as minor by team officials.
Australia team:
15-Ben Donaldson, 14-Mark Nawaqanitawase, 13-Jordan Petaia, 12-Samu Kerevi, 11-Marika Koroibete, 10-Carter Gordon, 9-Nic White, 8-Rob Valetini, 7-Fraser McReight, 6-Tom Hooper, 5-Richie Arnold, 4-Nick Frost, 3-James Slipper, 2-David Porecki (captain), 1-Angus Bell
Replacements: 16-Jordan Uelese, 17-Blake Schoupp, 18-Zane Nonggorr, 19-Matt Philip, 20-Rob Leota, 21-Issak Fines-Leleiwasa, 22-Lalakai Foketi, 23-Suliasi Vunivalu
