The Scottish-born forward, Boyle, who had been an injury doubt since the squad arrived in Qatar after suffering the injury playing for his club Hibernian, will be replaced by Marco Tilio (21).
"We all feel for Martin and it is a cruel blow for him on the eve of the World Cup," coach Graham Arnold said in a statement.
"He has been an integral part of our journey to get to Qatar and we thank him for everything he has given the Socceroos during this campaign.
"He will be back and we can't wait to see him in the green and gold again next year."
Tilio is in Qatar having arrived on Tuesday as precautionary cover for Boyle.
"Marco has done everything that has been asked of him to be ready for this tournament," Arnold said. "He was an important member of our Tokyo 2020 Olympic team ... and he is familiar with the national team set up and we are looking forward to what he can bring to our squad for the tournament."
