Art experts from the Gala-Salvador Dali Foundation knew that the two works existed but up until now they had been unable to locate and authenticate them.
"We had identified the works but we did not know where they were or how to link them to Dali. We thought they were made by him but we had to verify," the director of the foundation's research department, Montse Aguer, told news agency AFP.
"These are works from Dali's surrealist period. Both are very significant. They depict dreamlike landscapes that are typical of Dali, with shadows and big pedestals."
The two paintings were painted in 1930 and they were put on display by Dali only once, in separate exhibitions.
The Gala-Salvador Dali Foundation, located in the mustachioed artist's native Figueres in northeastern Spain, discovered the existence of the works through press clippings about the exhibitions that were published at the time.
One painting, "Free Inclination of Desire", which depicts a large rock along with ants, keys and other random objects, was shown in an exhibition in 1935 in Santa Cruz de Tenerife, the capital of Spain's Canary Islands.
It belongs to the art gallery of Yale University in New Haven, Connecticut.
The other painting, "Simulation of the Night", which depicts a veined hand on a column in a barren landscape, appeared at an exhibition in San Francisco in 1965.
It is in the hands of a private collector who does not wish to be identified.
Dali, who is praised by some as a creative genius for his striking and bizarre images, died in Figueres in 1989 aged 85.
The news comes only days after the Spanish tax office said it may have found a Van Gogh in a safety deposit box during an investigation into tax fraud. The painting is yet to be authenticated.