The 60-year-old Spaniard, a triple winner of the endurance event and also a double world rally champion, was injured when his electric hybrid Audi rolled on the ninth stage in Saudi Arabia last Tuesday.
He asked to be able to continue, despite an attempt to airlift him to hospital, but had to retire when his car turned out to be beyond repair.
"On my return to Madrid from the Dakar Rally, the back pain I suffered after the incident of this year’s event persisted longer than usual," Sainz said on Twitter.
"Following medical advice, I underwent further checks to assess in detail the extent of the injury. Unfortunately, the results haven’t brought good news because I fractured the T5 and T6 vertebrae."
Sainz said both vertebrae were stable and his priority was to recover as soon as possible.
The rally finished on Sunday and was won by Qatar's Nasser Al-Attiyah for the fifth time.
