The Gresini rider had looked unlikely to race in MotoGP next season until a late reshuffle opened up a space at Valentino Rossi’s team.
He lost his seat at Gresini to Marc Marquez, who joins the Ducati satellite team after 11 years with the Honda factory squad.
Though he was briefly linked to the Honda seat left by Marquez, Luca Marini was confirmed as his replacement on Monday morning.
This paved the way for VR46 to confirm Di Giannantonio will ride for them in 2024.
The 25-year-old had a late-season surge in form, taking his maiden win at the penultimate round in Qatar.
After that race, Ducati sporting director Paolo Ciabatti told motogp.com it was “unacceptable” that Di Giannantonio could be left without a ride for next season.
Di Giannantonio also took second place in the season finale in Valencia before he was handed a three-second tyre pressure penalty which demoted him to fourth.
He finishes his second season in the premier class 12th in the standings with 151 points.
Speaking in Sunday’s press conference, Di Giannantonio remained coy about his future but said he would be present at Tuesday’s test.
He told Autosport: “Let’s say that if you find a nice looking guy playing around with a new bike on Tuesday, could be me.”
After the announcement on Monday, Di Giannantonio added: “I'm happy to join such a strong team as the Mooney VR46 Racing Team, I can learn a lot and I can't wait to start working together on this project, we can do really good things.
“In the last two seasons in MotoGP I have grown a lot and in this team I will certainly be able to mature further and achieve great results. I'm excited, I can't wait to meet all my new staff and crew and start working on the track. Thanks to everyone who made this possible.”
Team director Uccio Salucci said: “I am really happy to announce that Fabio will join our team.
“It was an unexpected arrival, at the last minute but I am satisfied that we have chosen him. He had a great end of the season, he didn't lose himself when things didn't go well and I'm sure he'll be able to feel at home here.
“On a motorsport level, he has proven to be among the fastest young Italians, he will continue to work with Ducati and the objective is to help him be not only competitive, but also consistent in his results.
“It is an ambitious project, it marks a turning point in the history of our team, but I am sure that we will all give our best to go in the same direction.”
