Ferguson told reporters following the match: "The stand-side linesman never gave us a thing all day. I think he had a shocking game. I'm disappointed in his performance, I really am.
"We've got that history with him. He never gave offside with (Didier) Drogba at Old Trafford when he was three yards offside. Everyone remembers that. I certainly do."
An FA statement reads: "The FA has today charged Sir Alex Ferguson in relation to post-match media comments made following Manchester United's game at Tottenham Hotspur on Sunday 20 January 2013.
"It is alleged the Manchester United manager breached FA Rule E3 in that he implied that the match official was motivated by bias. Ferguson has until 4pm on Friday 1 February 2013 to respond to the charge."
Ferguson has been banned from the touchline on five separate occasions in the past.