Aged 30 and 32, the two men "are Swedish citizens and live in Gothenburg" in the west of the country, said Ronnie Jacobsson, the prosecutor heading the investigation into "terrorist crimes" in Syria.
The two are suspected of committing murder in Syria in 2013, two years after the outbreak of a revolt that morphed into a civil war.
Police are now on the hunt for a third suspect whose nationality has not been specified.
In a joint operation with the police, Sapo also carried out searches in the Gothenburg area where the two men were arrested early Thursday.
Prosecutors and Franzen refused to reveal any further details about the accusations.
In February, a Syrian refugee in Sweden was sentenced to five years' prison for war crimes in his country, where he had tortured a fighter loyal to President Bashar al-Assad.