Ferguson was given a five match touchline ban and a £30,000 fine after he let his thoughts on referee Martin Atkinson be known to the public.
Following a 2-1 defeat away to Chelsea he said: "You want a fair referee, or a strong referee anyway - and we didn't get that. I must say, when I saw who the referee was I feared it. I feared the worst."
Ferguson decided not to appeal and in their full written reasons the commission criticised him for not softening his stance.
They stated: "Although he denied any intention to question Mr Atkinson's integrity, he should, at the very least, have realised the import of what he said.
"The commission also took the view that Sir Alex's comments undermined the attempts by the association, through its Respect campaign to encourage higher standards of behaviour within the game, including respect for officials."