In a tough blow for the midfielder, Antonis was driving to the airport on Sunday to travel to Japan when the accident occurred, with the 20-year-old taken to hospital having complained of head and neck pain.
Scans at the hospital cleared Antonis - who has three international caps - of any major injury but the youngster has still been withdrawn from the Socceroos squad after a consultation between Sydney medical staff and Australian coach Ange Postecoglou.
The Socceroos' boss has named Luzern midfielder Oliver Bozanic as Antonis' replacement in the squad.
The two Asian Cup fancies go head-to-head in Osaka on November 18.