"They broke up at the end of January and it's amicable," Cruise's sister and publicist Lee Anne DeVette told the magazine.
Cruise, 41, met the 29-year-old Spanish actress while they were filming Cameron Crowe's Vanilla Sky in 2000. The couple decided to start dating in 2001 after Cruise's decade-long marriage to Academy Award-winning actress Nicole Kidman fell apart.
Robert Garlock, spokesman for Cruz, said neither star is dating anyone else. "They remain good friends and still talk often," he told People. "There is no other person involved."
"The relationship just ran its course and they decided not to be girlfriend and boyfriend anymore," a source close to the couple told the magazine. "Through most of the relationship they were both shooting movies in separate part of the world."