The agreement for next season includes an option to extend the contract for 2022.
Miller won the German IDM 125ccc championship in 2011 and was runner-up in the 2014 Moto3 championship.
The Townsville racer made his MotoGP debut in 2015 at the age of 20 and joined Ducati in 2018 with the Pramac Racing Team, the factory-supported team of the Bologna manufacturer.
He has one MotoGP win to his name and finished last season eighth overall in the standings last year, taking five podiums.
Miller follows former MotoGP champ and fellow Australian Casey Stoner who last gave Ducati a taste of championship victory in 2007.
Dream come true
Dream come true for Miller
“I always had dreams of becoming a fully-fledged factory rider,” he says.
“Fair to say I didn’t think it would happen with me sitting at home in Townsville having not raced for six months, but 2020 has been a strange old year.
“But it’s done, and having my 2021 plans sorted out so early is so exciting with what I’ll be doing, and in many ways a dream come true for me.
“When I got to MotoGP in 2015, this is what I was always chasing, so to have it actually happening is a bit surreal. But it’s the reality, and it feels bloody good.”
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Ducati boss Claudio Domenicali says that since Jack arrived in the Pramac Racing Team, he has “grown steadily, proving himself one of the fastest and most talented riders in the championship”.
“So we are happy that he has agreed to ride the official Desmosedici GP bike of the Ducati Team next year,” he says.
“We are convinced that Jack has all the right skills to fight continuously for the positions that matter, in every race, starting already this season with the Desmosedici GP20 of the Pramac Racing Team, and taking a further step forward next year thanks to the support of the Ducati Team.”