The Australian Rugby Union (ARU) have said that Tune had damaged his ankle in training and was aiming to return to play for Queensland in the Super 12 season from next February.
The 39-test veteran was a try-scorer in the Wallabies' World Cup final win over France in Cardiff last year and had been named as a reserve for Australia's warm-up match against a President's XV in Tokyo on Saturday.
Australia are set to play tests in Paris, Edinburgh and London on 4, 11 and 18 November respectively.
Ankle problems
The 23-year-old hurt his ankle in April and was out of representative rugby for 14 weeks, returning for Australia's last three tests of the Tri-Nations series only to break down against South Africa in Durban.
"Frustrating is one way to describe the situation," said a downbeat Tune.
"You could say this year has not been the best from my personal perspective. It looks like I have a bit more rehabilitation work to do."
Australian coach Rod Macqueen said there was no need to acquiuire additions for the 27-man squad following Tune's flight home to Brisbane on Sunday.
Rugby league convert Andrew Walker, who made his test debut against New Zealand in Sydney in July, is in contention to play at wing or fullback and would take Tune's place for the Tokyo match the coach said.
Macqueen stated the injury was a huge disappointment and that Tune would require further rehabilitation "to ensure his long-term playing career".
"The injury could not have come at a worse time for the team considering the number of experienced players missing from the tour," Macqueen said.
Veterans Tim Horan, Jason Little, David Wilson and Richard Harry retired after the Tri-Nations series and Stephen Larkham and George Gregan are unavailable for the European tour because of injuries.