The German defender was suspended after accepting an FA charge of violent conduct for stamping on the Manchester United player during last Saturday's match at Craven Cottage.
Fulham had challenged the FA's right to deal with the case retrospectively, arguing it was similar to that involving Chelsea's Fernando Torres when he escaped action for scratching Jan Vertonghen because an official had seen part of the incident.
However, an FA regulatory commission dismissed Fulham's argument and imposed the ban.
New rules will come into force on November 22 allowing retrospective action in all cases, even where incidents have been partially seen.
"The commission felt that a distinction could and should be made between these two incidents in that the stamp made by Mr Riether on Mr Januzaj was one of a series of 'comings together' involving a number of players in a melee as opposed to the isolated 'coming together' of Mr Torres with Mr Vertonghen which involved just the two players," said the report.
"The referee clearly states in his written match report that the act of stamping was 'unseen by any of the match officials at the time' and having viewed the DVD footage of the incident the commission had no reason to disbelieve the referee given his position, distance from the melee and the fact that his view was likely to have been obscured."