De Villota, 33, was found dead in a hotel room in Seville, Spain on Friday. "I can confirm that her death was due to natural causes. The family has been informed," Dr Joaquin Lucena Romero, head of forensic services at the Institute for Legal Medicine, said.
Spaniard De Villota lost her right eye in a crash in July 2012 while testing for the Marussia team.
She suffered severe head and facial injuries after colliding with a lorry at Duxford Aerodrome, Cambridgeshire, but had been cleared to resume driving.
De Villota, who had been in motor-racing for 12 years, had previously competed in Spanish Formula 3 and the Daytona 24 Hours race in the United States.
Her dream of driving a Formula 1 car came two years ago when she tested a Renault.
A family statement read: "Dear friends: Maria is gone. She had to go to heaven with all of the angels."
De Villota, daughter of ex-Formula 1 driver Emilio, was reported to have been in Seville to launch her autobiography.
The police spokeswoman said De Villota's body was found at around 07:00 (06:00 BST) at the Hotel Sevilla Congresos in the southern Spanish city.
F1 teams and drivers have expressed their shock at the news of her death.
Spaniard Fernando Alonso, the Ferrari driver, said: "Today is a very sad day for Spanish sport. We have lost a fighter with a huge smile."
Martin Whitmarsh, the McLaren team boss and president of the Formula 1 Teams' Association (Fota), said F1 would discuss what would be the appropriate way to mark De Villota's death over the Japanese Grand Prix weekend but that it was not a simple decision. Martin said, "We will be talking amongst ourselves... You have to be careful; a lot of racers don't want these issues to detract from a race weekend... Everyone wants to demonstrate the right level of sympathy but the real racers would want the show to go on and wouldn't want a fuss to be made. It's not something we need to amplify, it's something we've got to be sensitive about."