He was fined 60,000 Australian dollars and later rejected an incentive-based contract with the ARU last month before finally agreeing to terms.
The 24-year-old said: "It's no secret that I have a strong passion and desire to represent Queensland and Australia. I love playing for the Reds and the Wallabies.
"It's a great feeling to know that things are sorted and now I can continue to improve as a player and as a member of the Queensland Reds and the Wallabies.
"I'm confident I'll front for round one in peak physical condition and primed to play the best rugby in my career."
Acting ARU chief executive Matt Carroll added: "This means Quade Cooper and the Reds can now focus entirely on the upcoming 2013 Super Rugby season.
"Quade can now look forward to getting back on the field next year and playing for the Reds and in turn stake his claim for re-selection in the Qantas Wallabies squad.
"Next year is an exciting year for Australian Rugby with the British and Irish Lions venturing to our shores for the first time since 2001."
Reds director of coaching Ewen McKenzie is looking forward to having Cooper and Will Genia, who recently signed a new deal, in the halves next season.
"We have been preparing as if Quade and Will were both going to be around next season, so nothing much changes in that respect," McKenzie said.
"Obviously we're targeting winning the championship next year, so it will be good to push on with our preparations without the peripheral noise.
"Even some of our Wallabies have started to filter back into the set up this week, so it's good for our environment and culture. We're all working towards 2013."
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
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Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
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The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.