The pair — Jon Lizarribar Lasarte, born 1976, and Ruben Gelbentzu Gonzalez, born 1974 — are accused of taking part in four attacks in 2002, the Interior Ministry said in a statement.
The attacks were directed against the University of Navarra, the department store El Corte Ingles of Zaragoza and two companies from the neighbouring province of Navarra, it said.
Spanish police struck at about (0100 GMT) in the Basque province of Gipuzkoa, acting on intelligence gathered from documents seized in France from members of the ETA leadership, the Spanish authorities said.
Prime Minister Mariano Rajoy's government said 36 ETA suspects had been arrested up to the end of May this year since it took power in December 2011.
Listed as a terrorist group by the European Union and the United States, ETA is blamed for 829 deaths in a four-decade campaign of bombings and shootings for independence for the Basque Country of northern Spain and southwestern France.
It declared in October 2011 a "definitive end" to its armed activity but has not formally disarmed or disbanded as the Spanish government demands.
ETA has not carried out an attack on Spanish soil since 2009 and some experts estimate it has only a few dozen members still at large after a string of arrests of its members over recent years.