The 26-year-old midfielder will be out of action for up to four weeks after having an injection to cure a tendonitis problem, which has troubled him since the start of the season. He did not play his first game for United until Aug 19.
The former Bayern Munich player managed just three games before sustaining a thigh injury in training with England ahead of the Sep 8 game against Israel.
Manchester United manager Alex Ferguson said: "That was an option we had from the very start if it surfaced again. He felt it in training so we decided to do something immediately."
The news means that England manager Steve McClaren could stick with the central midfield partnership of Steven Gerrard and Gareth Barry for the Oct 13 and 17 games.
McClaren is also monitoring injuries to captain John Terry (fractured cheekbone) and striker Michael Owen (hernia). England will definitely be without Emile Heskey because of a broken metatarsal.