The Aston Villa midfielder pulled up sore after Australia's 3-2 World Cup qualifier win over Saudi Arabia last week.
The Aston Villa midfielder pulled up sore after Australia's 3-2 World Cup qualifier win over Saudi Arabia last week and coach Ange Postecoglou said with the Socceroos to play at least four games in 13 days an unfit Jedinak was too much of a risk.
He will be replaced by Austrian-based midfielder James Jeggo.
"Losing Mile is a blow as he is not only an important member of the midfield but a great leader amongst the group," Postecoglou said.
"He has had a tough period since Christmas with his groin and we all agree it is in the best long-term interest of Mile and the Socceroos that he has a break to ensure he is ready for the new season."
Jedinak said he was disappointed not to lead his country at the Confederations Cup in Russia, kicking off on June 17.
"It is something we have been looking forward to and working towards since we won the Asian Cup," Jedinak said.
"But we have some crucial games coming up over the next 12 months leading into the World Cup, which I need to be fit and firing for.”
The Socceroos take on Brazil in Melbourne on Tuesday before departing for Russia on Wednesday where they face Germany, Cameroon and Chile in the group stage of the Confederations Cup.