The 27-year-old Coventry-born rider, who lives on the Isle of Man, will team up once again with Andrea Dovizioso after previously partnering the Italian at Tech 3 Yamaha.
Crutchlow leaves the French-based Tech 3 team after failing to persuade Yamaha to provide him with a factory machine for next season.
His place at Tech 3 goes to Spaniard Pol Esparago who joins another British rider, Bradley Smith, after agreeing a two-year deal.
A statement from Ducati Racing read: "Ducati has reached an agreement with Cal Crutchlow that will have the Briton campaigning the 2014 and 2015 MotoGP race seasons with the Ducati Team.
"Crutchlow will race alongside Andrea Dovizioso. The British rider and the Italian, who were team-mates in 2012, will work on developing the Desmosedici and growing Ducati's MotoGP project.
"The 2009 World Supersport champion and 2011 MotoGP Rookie of the Year, Crutchlow is presently enjoying his strongest GP season to date, sitting fifth in the championship points standings. He has posted four podium finishes in the first nine races, and he earned his first MotoGP pole position at the Dutch TT.
"The end of the 2013 season will also mark the completion of Nicky Hayden's five-year professional relationship with the Ducati Team. Ducati would like to thank Nicky for his contributions during that time, and everyone on the team and at Ducati Corse looks forward to giving him and Andrea their full support over the second half of the 2013 season."
Crutchlow's move to Ducati is seen as a gamble but comes after he saw little future with Yamaha.
With the Tech 3 team having lined up Esparago to join Smith and with the factory Yamaha seats occupied by Jorge Lorenzo and Valentino Rossi, there was no room for Crutchlow to remain with the Japanese manufacturer given his desire to race a full factory specification machine in 2014.
The Ducati is regarded as one of the more difficult machines to ride in the MotoGP paddock, with multiple world champion Rossi failing to win a world title when the Italian raced for the manufacturer in between two spells with Yamaha.