Left back Shaw, who missed most of last season with a broken leg, has featured in all three of Manchester United's Premier League matches this season and was named in manager Sam Allardyce's first England squad for the match in Trnava.
The 21-year-old sat out of training out Saturday as England's medical staff looked to manage his workload, before the FA said on the national team's official Twitter account (@England) that he had been withdrawn from the squad.
Manchester United added in a statement on their official Twitter handle(@ManUtd) that the move was "precautionary" and Shaw would be returning to train with his club.
Allardyce has already lost Fraser Forster for his first match in charge, with the goalkeeper leaving the camp to be replaced by his Southampton team mate Alex McCarthy after injuring his arm in training.
(Reporting by Ed Dove; Editing by Rex Gowar)
