Ferguson landed in hot water with the FA after blasting Atkinson's performance in the Red Devils' 2-1 defeat against Chelsea at Stamford Bridge earlier this month.
The United manager ignored advice from his club's legal department and vowed to contest charges of improper conduct, but has now been hit by a hefty ban as his team enter a critical phase of the season.
Ferguson had appeared to question Atkinson's integrity when he stated that he had wanted a "fair referee" to control the match with Chelsea.
The FA deemed Ferguson's criticism had gone too far and handed the Scot a three-match ban which will bar him from the dugout for United's games against Bolton, West Ham and Fulham.
However Ferguson's rant against Atkinson meant that a two-match suspended sentence against him for a previous criticism of Alan Wiley has also been enacted. The additional two-match ban means Ferguson will be barred from the touchline for United's FA Cup semi-final with Manchester City.