The Reading defender will not join up with Giovanni Trapattoni's 23-man party because of 'family reasons'.
A spokesman for the Football Association of Ireland said: "Stephen has withdrawn from the Ireland squad to face Sweden this Friday for family reasons.
"He has been in touch with the manager, who has given Stephen permission to stay at home on this occasion."
The players were due to meet up at their Portmarnock base on Sunday.
Aiden McGeady, Sean St Ledger and Joey O'Brien have already pulled out of the double header that also includes a trip to Austria.