The German defender appeared to stamp on Januzaj in the last minute of Fulham's 3-1 defeat to United, but the incident was not seen by referee Lee Probert or his assistants.
Previously Probert would have been asked to review all available footage of the incident and then ask what action he would have taken had he seen it.
But in a pilot project, an FA panel of three former referees - Steve Dunn, Eddie Wolstenholme and Alan Wiley - make a ruling on what they believe the official would have done had he seen it.
For an FA charge to follow, all three panel members must agree it is a sending-off offence. In the instance of Riether, the panel were of the unanimous decision that it was an act of violent conduct.
The defender has until 6pm on Tuesday to respond to the charge.
United boss David Moyes, speaking just before the FA confirmed the charge, said: "I hadn't seen it until after the game. It's a bad stamp and it does look deliberate but that's for the referee to sort of deal with on the day...or they look at it differently. It's over now.
"But I do think Adnan needs a little bit of protection or we are going to find he's getting kicked up and down. I do think he deserves a little more than he's getting at this present time.
"He gets kicked up and down in training every day and he gets on with it. He's learnt from the good professionals to get on with it and accept it. He only needs to look at Lionel Messi. He's the best at getting up. We hope Adnan, and I'm not comparing him to Messi - we hope he can react like Messi - but he does need protection.
"It's not a case of asking for protection. It's up to the referees to do what's right. But we will never ask for it."
An FA statement said: "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 November 2 2013.
"The charge is in relation to an incident involving the defender and United's Adnan Januzaj which occurred in added time of Saturday's match at Craven Cottage.
"Riether is the first player to have been charged retrospectively by the FA under a new pilot project for potential 'not seen' incidents in Premier League matches.
"Previously, where the match officials had confirmed to The FA that none of them had seen an incident, the match referee was then asked to review all available video evidence before being asked what action, if any, he would have taken had it been seen.
"Under the new process, if an incident has not been seen by the match officials, a three-man panel of former elite referees Steve Dunn, Eddie Wolstenholme and Alan Wiley will be asked by the FA to review it and advise what, if any action, they believe the match referee should have taken had it been witnessed at the time.
"The panel were of the unanimous decision that it was an act of violent conduct."