Hibernian winger Boyle, who scored twice against Lebanon last month and looked set to feature prominently in Graham Arnold's plans, dropped out of the 23-man squad after suffering a knee injury in last weekend's 5-0 friendly win over Oman.
Arnold is already without Huddersfield Town midfielder Aaron Mooy, while key attacker Mathew Leckie could be unavailable until the knockout rounds as he nurses a hamstring problem.
AEK Larnaca striker Giannou, who has scored once in six international appearances, edged out the likes of in-form Adelaide United winger Craig Goodwin and discarded Luzern target man Tomi Juric.
"Apostolos has been playing regularly in Cyprus with his club, as well as in the Europa League throughout 2018," Arnold said.
"He has arrived with the determination to impress and make the most of the opportunity.
"Our group has welcomed 'Apo' back into the Socceroos family and having been with us in Turkey, the [United Arab Emirates], and Kuwait earlier this year, Apo has a clear picture of how we work and the principles of play.
"We have spoken consistently about our player pool getting deeper and to add Apo to our attacking options, despite the unfortunate news for Martin [Boyle], is fantastic.
"Apo offers us something a little bit different in attack – he is a hard-working player who can press and has a sharp eye for goal."
The Socceroos commence their Asian Cup defence against Jordan on Sunday, with Palestine and Syria their other Group B opponents.