Holman suffered the problem in AZ Alkmaar's 3-1 win over PSV Eindhoven on Sunday and will be replaced by the uncapped Adam Sarota.
"Adam Sarota of FC Utrecht has joined the squad in Cardiff, replacing Brett Holman of AZ Alkmaar," a Football Federation Australia statement read.
"Holman strained a groin muscle in Sunday's Dutch Eredivisie match against PSV Eindhoven and has remained in Alkmaar to receive treatment."
The absence of the influential Holman, who scored twice at last summer's World Cup finals, will come as a blow to the Socceroos who are also without fellow attacking midfielder Harry Kewell as he looks for a new club.
While the 22-year-old Sarota has yet to win a first cap, he was called up by coach Holger Osieck for Australia's 2-1 friendly win over Germany in March.
The friendly international at the Cardiff City Stadium will mark the first meeting between Australia and Wales.