The incident occurred in injury time of Fulham's 3-1 defeat to United at Craven Cottage on Saturday, sparking unsavoury scenes between the two sets of players.
Referee Lee Probert did not punish Riether for the challenge, but United midfielder Marouane Fellaini has since claimed that the German should have received a red card for his actions.
And, after reviewing video evidence of the incident, the Football Association has elected to charge the former Hamburg man, who has until Tuesday to respond.
A statement on the FA website read: "Fulham's Sascha Riether has been charged by The FA for violent conduct following an incident which was not seen by the match officials but caught on video during his side's game against Manchester United on 2 November 2013.
"The charge is in relation to an incident involving Riether and United's Adnan Januzaj which occurred in added time of Saturday's match at Craven Cottage.
"The defender has until 6pm on Tuesday 5 November 2013 to respond to the charge."
Riether has made 11 appearances for Fulham this season.
