The 31-year-old was charged on Monday after catching West Ham's Winston Reid with his left arm as they waited for a free-kick to be taken during Saturday's 0-0 draw at Old Trafford.
The Germany international will face a three-match ban if found guilty.
He has until 12:00 GMT on Thursday to respond to the charge.
Referee Mark Clattenburg spoke to both players after the incident, but did not mention it in his post-match report.
"The matter was referred to a panel of three former elite referees who each reviewed the video footage independently of one another to determine whether they considered it a sending-off offence," said an FA statement.
"For an FA charge to follow the decision by the panel must be unanimous."
Manchester United midfielder Bastian Schweinsteiger is likely to appeal after being charged with violent conduct by the Football Association.