Enlargement Commissioner Olli Rehn and Serbian Deputy Prime Minister Bozidar Djelic initialed the Stabilization and Association Agreement (SAA) following approval from Carla Del Ponte, the chief prosecutor at the International Criminal Tribunal for the former Yugoslavia (ICTY).
Del Ponte said she was satisfied that Serbian authorities were willing to hand over to the Tribunal the four remaining fugitives accused of war crimes.
Human Rights Watch criticized the move despite assurances from EU officials that the SAA would only be signed after all the fugitives had been handed over to the tribunal.
"This sends the message that the EU is prepared to let those who commit horrific crimes wait out justice," an organization statement said.
Although the agreement is another step towards Serbian membership to the EU, the Balkan nation is not expected to join before 2014.