The 29-year-old loose forward only made his international debut last year before he was sensationally vaulted into the captaincy role by coach Ewen McKenzie as he shook up the team after replacing New Zealander Robbie Deans in July.
"While my desire to play for Australia is still extremely strong, my priority is to spend more time with my wife and our daughter," Mowen said in an Australian Rugby Union statement.
"I would have loved my career to have lined up to help Australia win the next rugby World Cup, but my priority at this stage in my life is my family.
"I will be cheering hard from a distance - we have the squad and coaching staff to achieve a Rugby World Cup win in 2015 and I wish them all the very best."
Mowen was a successful leader of the ACT Brumbies, taking them to the Super Rugby final against the Waikato Chiefs before he was named by Deans in the Wallabies team to play the British and Irish Lions.
Mowen was handed the captaincy during the Rugby Championship for one match when regular skipper James Horwill was injured before McKenzie stripped Horwill of the leadership role on the team's northern hemisphere tour in November.
Mowen is to join a French club at the conclusion of his commitments in Australia, which would rule him out of Wallabies selection for the World Cup in England in 2015.
The Australian Rugby Union has a policy of picking only players based in Australia and McKenzie has said he expects his World Cup squad to be drawn from players involved in Super Rugby in 2015.
"It's obviously disappointing to lose a player of Ben's calibre," McKenzie said.
"But after speaking to him about his personal priorities, we appreciate that he is making this decision based on what is right for him personally and professionally."