The attacking midfielder, who would almost certainly have started the match after a successful season with Scottish champions Celtic, cited personal reasons for his withdrawal from the June 7 match.
No replacement will be added to the squad, which is already in Doha preparing for the game, and coach Graham Arnold said Rogic's withdrawal was "unfortunate."
"My focus must now be on the players we have here in Qatar," Arnold said in a Football Australia statement.
"We have selected an extended squad of quality players and I believe that we will achieve something special for Australia over the next two weeks."
The winners of the match will take on Peru in an intercontinental playoff in the Qatari capital six days later for a spot in the finals.