Police say 950 demonstrators gathered in Saint-Jean-Pied-de-Port, while organisers have put the figure at 2,000.
The event was organised in support of Xabier Goyenechea, 35, and Joseba Inaki Reta, 56, who were arrested 8 July in the village of Ossès.
The two were responsible for the logistics unit of Eta, according to the Spanish Interior Ministry, while Goyenechea was also involved in the theft of six vehicles from a garage near Paris, during which a French police officer was killed.
The pair have been indicted by a Parisian anti-terrorist investigating judge and imprisoned for criminal conspiracy, possession and transportation of weapons and false record keeping, all in relation to a terrorist enterprise.
Home owners in Ossès who housed them have also been indicted in the case.
The arrests have provoked clashes between Basque nationalists and police.
The raid is the latest by anti-terror police who in May uncovered an arms cache in the French west coast town of Biarritz.
Eta renounced armed struggle in 2011 but has refused to dissolve itself or surrender its arms.
It started a unilateral decommissioning process in 2014 but has refused to hand over its weapons to the regional government of the Spanish Basque country.
The group is blamed for the deaths of 829 people in a four-decade campaign of shootings and bombings to create an independent Basque homeland in an area of northern Spain and southern France.