The Red Devils boss was furious after his side conceded a late equaliser at Tottenham in January - insisting the visitors should have been awarded a penalty for Steven Caulker's trip on Wayne Rooney.
Referee's assistant Simon Beck was the subject of the ire of the Scot, who said in the wake of the 1-1 draw: "It was a clear decision. And he [Beck] was 10, maybe 12 yards away from the incident and he doesn't give it. And yet he gave everything else."
"There was no way we were going to get a decision from [Beck].
"We remember him well from his time at the Chelsea game when Didier Drogba was three yards offside and he gave onside. I think he had a shocking game today, and I'm disappointed in his performance, I really am.
"I think he has had a bad game, and we never got anything from that side of the pitch. We got a bad break."
The FA charged Ferguson with a breach of rule E3, and have subsequently found him guilty at a private hearing despite his pleas to the contrary.
The news of the fine came through after Ferguson criticised England Under-21 coach Stuart Pearce for disclosing that Phil Jones was suffering from shingles.
Jones withdrew from the Under-21 friendly with Sweden on Tuesday which prompted Pearce to reveal the nature of the 20-year-old former Blackburn player's injury.
However, the problem is evidently not as bad as first feared as Ferguson has named Jones, who can play in defence or midfield, in his squad to face Everton in the Premier League on Sunday.
And Ferguson is not happy with the way the situation has been handled.
"What about doctor confidentiality?" said the United boss."Jones is fine despite what Stuart Pearce says and we're very disappointed with the FA for that."
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Premier League Without Manchester (City and United)12/13 Win Outright: Chelsea 2/7
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