His place in the 13-man squad for the match starting on Thursday at Lord's goes go Hampshire seamer Chris Tremlett.
Harmison was assessed by a member of England's medical staff on Sunday and will find out on Tuesday if he needs surgery.
In an ECB statement chairman of selectors David Graveney said: "We have taken the precaution of adding Chris Tremlett to the squad following confirmation this morning that Stephen Harmison will not be available.
"Chris performed well in the recent England Lions tour match against India and his inclusion will give us additional options when we come to decide on our starting eleven."
