The crew of a search helicopter found the husband and wife, from Qatar, near the couple's overturned vehicle.
It appeared the man tried to find help or water on foot and died about 6 miles from the wreck. The woman's body was recovered at the crash scene.
The BBC said a massive search was launched after a relative of the couple reported them missing.
The Empty Quarter is virtually uninhabited with scorching heat, towering sand dunes and less than an inch of rain per year, the BBC said.