Boyle has been a breath of fresh during his three Socceroo appearances and managed to score a brace in his only start versus Lebanon at Sydney's ANZ Stadium in November.
He joins playmaker Aaron Mooy and exciting winger Daniel Arzani as crucial green and gold absentees, while there is still injury clouds over Mathew Leckie and Tom Rogic.
"We sent Martin [Boyle] for a scan yesterday and the outcome of that assessment is that he will be out of action for an indefinite period," Socceroos coach Graham Arnold said via a statement.
"Martin was desperate to stay with us but we've decided that the best thing for his long-term career for both his club and country is for him to return to Scotland where he can receive great care at Hibernian.
"Martin has made a great impact in his time with us and it is unfortunate timing, but his Socceroos journey is not over and we look forward to him pressing for selection for matches later in 2019 and as we go through the process of qualification for the next FIFA World Cup."
Boyle revealed his anguish at the forced late withdrawal but said he would be fully behind the green and gold as they aim to win their second consecutive Asian Cup.
"The Socceroos have become a big part of my life in a short period of time and I'm gutted that I won't be able to be with the boys in the UAE at the tournament," he said.
"My focus now will be on my recovery and returning to the pitch as soon as possible with Hibs. Throughout the tournament the team will have my full support from Scotland."
A replacement for Boyle will be revealed over the coming days with Adelaide United winger Craig Goodwin and Newcastle Jets playmaker Dimitri Petratos the favourites to come into the squad.
Australia's first Asian Cup match will come against Jordan in Al-Ain on January 6.