Ferguson was charged on Thursday over comments he made about referee Martin Atkinson after this week's 2-1 defeat at Chelsea in which he said he had "feared the worst" when he had seen who was officiating the match.
The Scot cancelled his customary pre-game news conference on Friday while he considered whether to appeal with a club spokeswoman later confirming in an email that "Yes, he has" decided to appeal.
The Scot was also angry that Chelsea's Brazilian defender David Luiz, who had equalised, escaped a red card for a second-half challenge on Wayne Rooney.
"It was a major game for both clubs and you want a fair referee," Ferguson said. "You want a strong referee anyway and we didn't get that."
Ferguson had shunned the media spotlight on Friday, cancelling a news conference where he would have been expected to talk about Sunday's Premier League match against Liverpool. Local media also reported he was not even speaking to the club's in-house television channel MUTV.
With 60 points, they have a four-point lead over second-placed Arsenal but Arsene Wenger's side have a game in hand.
By the time Ferguson's team kick off at Anfield on Sunday, against the rivals who will be hoping to derail United's bid to beat the championship record they currently share, their lead could have been cut to one point as Arsenal play on Saturday.
