Rescuers using heavy lifters are continuing to search for the bodies of two men believed to have been killed in the blast.
It was the strongest language by a government minister since the bombing that wrecked a car park at a new terminal at Madrid's Barajas airport.
Hours after the bombing, Jose Luis Rodriguez Zapatero, the Spanish prime minister, suspended all efforts to seek dialogue with Eta, ending a peace process begun in June after the group declared a ceasefire in March.
Zapatero's response was criticised by the conservative opposition Popular Party, which had opposed talks with Eta from the start and demanded the government now unequivocally declare the peace process dead.
Rubalcaba called for a unified approach following the bombing.
He said: "Obviously the process has finished.
"And now I've cleared that up, it would be fantastic if we could all work together to put an end to violence in Spain."
Basque independence
Eta has killed over 800 people in four decades of violent struggle for independence for the Basque Country in northern Spain and southwest France.
Its fight began during Franco's dictatorship when the Basque language and culture were suppressed.
In today's democratic Spain, only a minority of Basques want full independence, according to opinion polls.
In recent years, Spanish and French police have arrested hundreds of members of the group, gutting its operational ability.