Riether has been banned for stamping on Manchester United's Adnan Januzaj in the Premier League clash between the two sides last weekend.
The German defender's action was not seen by the match officials but was caught on video.
An FA statement said: "Following an independent regulatory commission hearing today, Fulham's Sascha Riether has been suspended for three matches with immediate effect after he accepted an FA charge for violent conduct.
"Riether was charged by the FA following an incident which occurred in added time of Fulham's game against Manchester United on Saturday 2 November 2013. The incident, which involved United's Adnan Januzaj, was not seen by the match officials but was caught on video."
Fulham initially queried whether they had to accept the charge and asked for clarification from the FA on its retrospective action rule.
Riether, 30, was the first player to be charged by the FA under a new pilot scheme where a panel of three former referees reviews video evidence of incidents not seen by match officials.
The German full-back apologised for stamping on Januzaj via his official Twitter account on Tuesday, adding: "I will accept the consequences of my actions, and hope to put it behind me when I return."
Despite Riether's admittance of guilt, it is understood the club did not accept the charge before Tuesday's 6pm deadline and instead asked for clarification on certain points of the newly-instigated rules that govern when action can be taken.