Allen was named in the initial 23-man squad to take on Macedonia and Serbia next month but will now be forced to miss out due to a hamstring injury suffered in Liverpool's League Cup match against Notts County on Tuesday.
The 23-year-old joins Swansea City's Neil Taylor in withdrawing from the squad, with the latter suffering from a thigh injury.
"Liverpool's Joe Allen will be forced to miss the FIFA World Cup qualifiers against Macedonia and Serbia," read a statement on the Welsh FA's official website.
"Allen was injured playing for his club against Notts County at Anfield on Tuesday night in the Capital One Cup.
"He joins Swansea City's Neil Taylor on the sidelines."