The court overturned a ruling, which found three of the men guilty of being members of the radical cell linked to al-Qaida. A fourth man was cleared of trafficking explosives.
On Oct. 31 last year, Spain's anti-terrorist court convicted 21people of involvement, and acquitted six others.
The supreme court overturned the convictions of Basel Ghalyoun and Mohamed Almallah Dabas, both condemned to 12 years in prison for belonging to a terrorist group.
Raul Gonzalez, a Spaniard, was acquitted of supplying explosives.
The court also upheld the acquittal of "Mohamed the Egyptian," Rabei Osman Sayed Ahmed, who was accused of being one of the masterminds behind the bombings.
