The omission of flanker Hooper, who has captained the Wallabies for the best part of the last decade, and 80-cap flyhalf Cooper were only the headline surprises as Jones made a statement with his selection.
"The experts have written us off. No one believes we can do it, but we believe," Jones said in a press release.
"I've backed the young blokes because they earned it. Simple as that. I haven't handed it to them. They grabbed it. It's exciting for me to go to work each day with these guys who are just busting to improve, to learn and to get better."
Australia, world champions in 1991 and 1999, are languishing in eighth place in the world rankings and have yet to win a test in four attempts since the return of Jones as coach in January.
Cooper had long been expected to be Australia's starting flyhalf in France after recovering from a ruptured Achilles to return to the squad.
Carter Gordon, who played his first test last month, will now travel to France as Australia's sole specialist flyhalf with Ben Donaldson, who has played two internationals, backing up as a utility.
Uncapped teenager Max Jorgensen was also named in the squad as an outside back despite having played only a handful of Super Rugby matches before his season was cut short by a knee injury sustained in late May.
There was also a surprise in the captaincy with France-based lock Will Skelton taking the role in partnership with scrumhalf Tate McDermott, who led the side for the first time against the All Blacks last week.
Hooper, who has played 125 times for Australia since 2012, was named co-captain of the Wallabies with James Slipper for the Rugby Championship but played in only the opening loss to South Africa before being sidelined by a calf injury.
Tom Hooper and Fraser McReight, Hooper's replacements in the back row for Australia's last three tests, were included, as was three-cap loose forward Langi Gleeson.
Jones included two other uncapped players in his squad, with Issak Fines-Leleiwasa one of three scrum halves selected and Blake Schoupp the least experienced of a largely inexperienced group of six props.
Slipper, who has played 131 tests, is one exception with Taniela Tupou the other. Tighthead Tupou suffered a rib injury against the All Blacks two weeks ago on his long-awaited return from an Achilles injury.
The 33-man squad has an average age of 26 with an average of 20 test caps per player - the lowest at a World Cup for Australia since the 1991 edition.
"The team that improves the most is generally the team that will win it and that's the task we have set ourselves," said Jones.
"We have been improving and we will continue to improve."
Australia will face Wales, Fiji, Georgia and Portugal in the opening round of the Sept. 8-Oct. 28 tournament.
Australia's World Cup squad:
Forwards: James Slipper, Taniela Tupou, Pone Fa'amausili, Zane Nonggorr, Blake Schoupp, Angus Bell, Dave Porecki, Matt Faessler, Jordan Uelese, Richie Arnold, Nick Frost, Will Skelton, Matt Philip, Fraser McReight, Tom Hooper, Rob Valetini, Josh Kemeny, Rob Leota, Langi Gleeson.
Backs: Issak Fines-Leleiwasa, Tate McDermott, Nic White, Carter Gordon, Ben Donaldson, Lalakai Foketi, Izaia Perese, Samu Kerevi, Jordan Petaia, Max Jorgensen, Andrew Kellaway, Marika Koroibete, Mark Nawaqanitawase, Suliasi Vunivalu.
