Madrid says that Sorzabal, 43, and Pla, 40, were the political leaders of Eta, the organisation that waged an armed struggle for independence from Spain for 50 years before renouncing violence in 2011.
French and Spanish police have been looking for Sorzabal for at least 10 years and Pla has been living underground for four years, sources say.
Sorzabal has been given several prison sentences in France for Eta membership and she is suspected of having taken part in several attacks and assassinations.
The pair are said to have made up Eta's executive committee and, according to Spanish daily El Pais, they announced the "definitive end of armed actions" in 2011.
But no agreement has been reached between the group and the Spanish government, partly because Eta refuses to hand over its weapons.
After the arrests on Tuesday, Spanish Interior Minister Jorge Fernandez Diaz declared that the organisation had been "decapitated" and was a "corpse".
"All that's missing is the death certificate," he said.
The two other men who were arraigned are Patxo Flores and Ramon Zagarzazu.
Flores, 45, who is French, put Sorzabal and Pla up in a guest house in the French Basque country and was arrested in 2007 in connection with an attack on chef Alain Ducasse's restaurant in the region.
Zgarzazu, a 49-year-old Spaniard, served 10 years in prison in France and is believed to be the head of Eta's international section.