The 29-year-old loose forward made his test debut against the Lions last year, making 15 appearances for his country in 2013.
He replaced James Horwill as Wallabies' captain for the end-of-year tour. Australia lost their first test to England under his charge before beating Italy, Ireland, Scotland and Wales.
Mowen is expected to sign with a French club after taking part in the Brumbies' 2014 Super 15 campaign.