Farrell's shoulder made contact with the jaw of Jack Clement as the former England captain attempted a tackle.
The TMO brought the incident to the attention of the referee, but he ruled that it had taken place too far back in play for any action to be taken at the time.
On Monday, however, the RFU announced that Farrell had been cited for "dangerous tackling", with a hearing scheduled for Tuesday evening.
If Farrell is found guilty he is likely to face a ban of several weeks. A two-week ban would impact his Saracens appearances but leave him free for selection for England, whereas a month ban would rule him out of the Twickenham game with Scotland.
Farrell, who has been in brilliant form at flyhalf for table-topping Saracens this season, was a regular at inside centre for England under Eddie Jones, with Marcus Smith preferred at 10.
Smith has not played since November due to an ankle injury but is expected to return for Harlequins this weekend.
New England head coach Steve Borthwick will announce his Six Nations squad next Monday.
