Greek police shut down roads around the embassy as white-clad forensic experts searched through the driving rain for clues of the attackers.
Police said the attackers were probably on motorbikes and were armed with Kalashnikov rifles. More than a dozen shell casings were found at the scene.
The Greek Foreign Ministry “unequivocally condemned the attack” and vowed that it would not harm burgeoning Greek-Israeli relations.
“The immediate mobilization of the Greek Police, who are fighting terrorism in a coordinated and effective manner, will bring the perpetrators before the Greek justice system,” the statement said.
The embassy also expressed “full confidence that the Hellenic Police and Authorities will deal with this incident.”
The embassy was closed at the time of the attack in the early morning hours.
There was no claim of responsibility and it was not immediately clear who was behind the attack.
Greek anarchist groups have attacked several foreign embassies in Athens in recent years, and there was a similar shooting attack on the home of the German ambassador last year.
However, Friday’s attack also comes amid increased tensions after the death of a Palestinian minister that Palestinians have blamed on Israeli soldiers.