Paul will be rested from the November matches against France, England, Ireland and Wales due to a minor neck injury.
The 28-year-old has been capped 63 times by his country, scoring 12 tries, since making his international debut against Scotland in 1998.
Wallabies coach Eddie Jones said: "The advice from the medical staff is to give Jeremy the opportunity to rest his injury and unfortunately that means missing out on the tour.
"The good news at this stage is that it's not something too serious, and with some rest and a break from the game, he should be right to start the Super 14 next season."
Hookers Brendan Cannon, Adam Freier, Stephen Moore and Tatafu Polota-Nau are included in Australia's 44-man training squad ahead of the trip to Europe.