Ferguson was charged following his criticism of assistant official Simon Beck after United were held 1-1 by Tottenham at White Hart Lane on January 20.
The United manager was angered by Beck's refusal to flag for a penalty when Steven Caulker was involved in a challenge with Wayne Rooney.
Ferguson said following the final whistle: "The stand-side linesman didn't give us a thing all day. For me it was a poor performance by him.
"Why he never saw the penalty kick from Wayne Rooney and some other decisions … We remember him well from his time at the Chelsea game when Drogba was three yards offside and he gave onside.
"He had a shocking game. I'm disappointed in his performance, I really am. He had a bad game and we never got anything on that side of the pitch."
Ferguson appealed against the charge that followed and requested a paper hearing. However, the verdict, which has been released by the FA this afternoon, has gone against the Scot.
An FA statement read: "Following an Independent Regulatory Commission hearing today, Sir Alex Ferguson has been fined £12,000 in relation to media comments made after Manchester United’s game at Tottenham Hotspur on 20 January 2013.
"It was alleged that the Manchester United manager’s post-match media comments implied that the match official was motivated by bias.
"Ferguson had denied the misconduct charge and requested a paper hearing at which the Independent Regulatory Commission found proven the breach of FA Rule E3."