The agreement takes the New Zealand-born playmaker through until the end of the 2019 rugby World Cup in Japan.
The 28 year old re-joined the Wallabies ahead of the Rugby Championship and started at first-five in last weekend's second Bledisloe Cup test defeat to the All Blacks in Wellington.
"For me, playing at the highest level for the Wallabies against the best teams in the world, week in, week out is the ultimate, and it will always be the pinnacle of our sport," Cooper said.