The decision to dig up the body was taken after her brother questioned the cause of death, alleging that she had been poisoned.
Reports at the time suggested that Felix, who charmed cinema audiences throughout the Hispanic world for decades, had died of a heart attack.
There is tight security around the cemetery in Mexico City, where a makeshift autopsy tent has been erected. Around 100 riot police have been mobilised to protect forensic scientists as they work.
The film star died in her sleep on her 88th birthday, 8 April, bringing Mexico to a virtual standstill.
Correspondents say it is unclear who or why someone might have tried to kill her.
But brother Benjamin Felix says he and other family members were prevented from seeing her body after she died.
The autopsy results will not be known for at least a week.
Strong and silent
Felix was renowned as a femme fatale and the one-time lover of the painter Diego Rivera. Her four turbulent marriages also regularly made headlines.
She made 47 films in her career though few of them were shown widely outside Spanish-speaking nations.
Felix often portrayed strong, silent women, endowed with intelligence and a voluptuous glamour.
Born in 1914 in Alamos, northern Sonora state, her real name was Maria de los Angeles Felix Guerena but she became affectionately known as La Dona, or The Dame in Mexico after her film hit Dona Barbara in 1943.
She also had a home in Paris where she spent half the year and in 1996 France awarded her the nation's highest distinction, the National Order of Arts and Letters.
Felix last starred in La Generala (The Lady General) in 1970.