The United manager was sent to the stands at half-time during the Premier League champions' 1-0 defeat at Bolton Wanderers last month.
Ferguson was unhappy with the 'aggressive' tactics being deployed by Bolton, with Kevin Davies' running duel with Patrice Evra a source of discontent.
An FA statement read: "At a Regulatory Commission hearing yesterday, Manchester United manager Sir Alex Ferguson was given a two-match touchline ban, starting on Friday 28 December. He was also fined £5,000.
"As he did not request a personal hearing, the case was dealt with on the basis of written statements and video footage."