The American will be joined at the outfit by Italian Moto2 race-winner Andrea Iannone.
It had long been rumoured that Ducati could set up a junior team for 2013. While the new squad does not bear the moniker, it will - as was expected of the junior team - enjoy close factory links, with Ducati supplying both riders with official equipment.
Pramac, which has run Spaniard Hector Barbera in this year's championship, will be entrusted to operate the duo.
Spies had been connected with a switch to Ducati ever since announcing his departure from the works Yamaha squad on the eve of the US Grand Prix at Laguna Seca.
At the same time however he has also been linked with a move to World Superbikes, having endured a torrid season.
He has retired from the last three grands prix, suffering an engine failure while running second at Indianapolis and crashing out after struggling with a slipping clutch at Brno.
Spies' arrival at Ducati's satellite operation follows from August's confirmation that Andrea Dovizioso will replace the outgoing Valentino Rossi in the works squad.
23-year-old Iannone meanwhile steps up into MotoGP after impressing during a recent private test at Mugello.
He becomes the second Moto2 rider to move onto a prototype machine in 2013, following confirmation of Moto2 championship leader Marc Marquez's move into the works Honda team as a replacement for the outgoing Casey Stoner.
In an official statement, Ducati said closer links with a satellite operation would "enable additional important support in the development of the Desmosedici MotoGP project."
Ducati has already committed to re-organising its racing department in order to take full advantage of its relationship with Audi.