 The men were arrested after a request from French authorities
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Spanish officials say four of the men were arrested in the south-western city of Valencia, and the fifth in the northern town of Logrono in the Rioja region.
Police searched the homes of the suspects and confiscated documents and other items, a Spanish interior ministry spokesman said.
Al-Qaeda was reported last year to have claimed responsibility for the truck bombing of the El Ghriba synagogue, in which 14 German and two French citizens were killed.
Reports say Spanish judge Ismael Moreno ordered the arrests after a request from French authorities investigating the attack in Djerba.
France's top anti-terror judge, Jean-Louis Bruguiere, opened his own investigation into the attack after the son of one of the victims filed a complaint in a French court.
France also wants to question the alleged senior al-Qaeda operative captured in Pakistan last weekend, Khalid Sheikh Mohammed, about the bombing.
Sheikh Mohammed is believed to have given the order by satellite telephone to the suspect who carried out the attack, French judicial officials said earlier this week in Paris.
Previous arrests
Saturday's arrests follow the detention in late January of 16 men in Spain's north-eastern region of Catalonia for alleged links to al-Qaeda.
Those arrests were also made using information from French authorities.
So far reports say the only crime committed by those men, who are still in police custody, is forging identity cards.