Ferguson had called Webb "the best referee in the country" before the official took charge of United's 2-1 Premier League victory over Chelsea on May 8, while Ancelotti described him as a "fantastic referee" prior to the Old Trafford meeting.
FA regulations make it clear managers are not allowed to comment on referees before a game, regardless of whether the statements are positive or negative, and the FA said it wanted to send a message out to managers to watch what they say.
Regarding Ferguson's case, the chairman of the FA's regulatory commission said in a statement: "This is a clear breach of the rule and it is the first time such a matter has been placed in front of a commission."
"As a result of this charge, the commission were aware of other occasions where pre-match comments were made by other managers.
"In this case, it was considered to be a minor breach, but a breach nevertheless, and it should be taken as a warning to all managers in the future that any such breach, even positive comments, are likely to result in a charge by the FA."
Later on Tuesday, the FA announced it had also warned Ancelotti "as to his future conduct" for comments he made at a news conference on the same day as Ferguson's remarks.
Ferguson is unlikely to let the warning spoil his jubilant mood after leading United to a record 19th league title at the weekend but he may be more careful about what he says before Sunday's final league game of the season against Blackpool.
