Greek minister for citizen protection, Nikos Toskas, said in a statement that one of the men had been registered on the Greek island of Leros in October.
"We confirm that the (Syrian) passport holder came through the Greek island of Leros on October 3 where he was registered under EU rules," said a statement issued by Toskas.
French police said the passport was found "near the body of one of the attackers" in the investigation into the main attack of Friday's carnage, at the Bataclan concert hall, where 82 people were killed.
The authenticity of the passport was being checked, but its discovery indicates a possible Syrian connection which has been a working hypothesis for investigators after assailants hit six separate locations in Paris.
A Greek police source said the second man had also registered in Greece, with TV station Mega adding this was also on Leros in August.
European security officials had long feared that jihadists could take advantage of the mass migration influx, mainly from war-torn Syria, that Europe has been experiencing since the beginning of the year.