Moore, who was appointed as captain before the series, tore ligaments in his left knee early in the first test and will require season-ending surgery.
Openside flanker Michael Hooper was named to replace Moore as skipper on Monday.
Carter suffered a high ankle sprain in the match and was ruled out for the rest of the series. His place in the starting side for Melbourne has been taken by former captain James Horwill.
Palu also suffered his injury at Lang Park but should be available for the third test in Sydney on June 21. He was replaced by Ben McCalman in the starting side.
"It's disappointing to lose three key forwards through injury, but in Tatafu, James and Ben, we're bringing in a collective 126 game of international test experience," McKenzie said in a statement.
"They understand what test rugby is all about and will be determined to make the most of the opportunities they're being given."
The clash in Melbourne will be Horwill's 50th test appearance for the Wallabies.
McKenzie introduced three uncapped players onto his replacements bench with hooker Nathan Charles, prop Laurie Weeks and lock Luke Jones in line for their test debuts.
While the Wallabies were rampant in their first test victory, McKenzie said he expected a far improved French side would be on the field on Saturday.
"France is one of the few one teams in the world who can make a lot of changes and still turn things around quickly in one week," McKenzie said.
"They never stay down for long and will be using the disappointment of the opening test to motivate them for the second game.
"We were pleased with our performance on a short preparation but we understand that we must improve if were going to match a reinvigorated and desperate French line-up on Saturday."
Australia: 15-Israel Folau, 14-Adam Ashley-Cooper, 13-Tevita Kuridrani, 12-Matt Toomua, 11-Nick Cummins, 10-Bernard Foley, 9-Nic White, 8-Ben McCalman, 7-Michael Hooper (captain), 6-Scott Fardy, 5-James Horwill, 4-Rob Simmons, 3-Sekope Kepu, 2-Tatafu Polota-Nau, 1-James Slipper
Replacements: 16-Nathan Charles, 17-Pek Cowan, 18-Laurie Weeks, 19-Luke Jones, 20-Scott Higginbotham, 21-Nick Phipps, 22-Kurtley Beale, 23-Pat McCabe
(Reporting by Greg Stutchbury in Wellington; Editing by Julian Linden)
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