A Spanish judge ordered the exhumation when litigation was brought forth by Pilar Abel, who said she was born after her mother, Antonia, had an affair with Dali while she was working for his family in the 1950s, according to NBC News.
Almost three decades after his death, the Spanish painter's body, mummified after an embalming process, is "in good condition", said Marta Felip, mayor of Figueres, who was present at the late-night exhumation in the Catalonian City's Dali Theater and Museum.
In June, a Madrid judge ruled a DNA test should be performed to find out whether her allegations were true.
"I'm very certain that the results are going to turn out to be positive", she told Spanish La Sexta network in a recent interview.
She said she was looking forward "to the truth being known once and for all".
The case came about after Pilar Abel, a psychic who worked in Catalonia claimed that her mother has a relationship with the surrealist painter in the port of Cadaques, Spain, where he lived for years.
Dali died in 1989 and was buried in Figueres, the town where he was born 84 years earlier.
Dali's estate, which includes properties and hundreds of paintings, is entirely in the hands of the Spanish state. The building now hosts the Dali Theater Museum.
After the gates of the premises closed Thursday, a 1.5-ton stone slab was removed to open the crypt where Dali was interred 27 years ago.
It remains to be seen if the chemicals used for preserving the artist's body have damaged his genetic information, said Narcis Bardalet, the forensic expert who embalmed Dali back in 1989.
"He would feel at home, it is a day that suits his way of being", Lorca said.
The Gala-Salvador Dali Foundation is expected on Friday to make a statement to journalists about the exhumation. Before work in the crypt began on Thursday, mobile phones were put in a deposit and the museum's glass dome was covered to prevent drone photography or videos.
The sample will be sent to Madrid, where it will be analyzed for a match with the DNA in a saliva sample provided by Maria Pilar Abel, 61.
Dali's paternity lawsuit was a topic of discussion Thursday among the lines of visitors at the museum.
For more than a decade, Ms Abel has claimed that she is the product of a clandestine love affair between her domestic worker mother and the artist, who was then living with his wife Gala. "But I think it is surreal that they have to unearth his body after such a long time".