Ferguson was furious with Atkinson for awarding the 76th minute free-kick that led to Chelsea's winner, scored by John Terry, at Stamford Bridge on Sunday.
"The referee's position to make the decision was absolutely ridiculous, he can't see anything," Ferguson said. He's got a Chelsea player (Joe Cole) standing right in front of him and he doesn't even move.
"That goal shouldn't have been allowed. It was a bad decision, but there's nothing we can do about it. You lose faith in refereeing sometimes, that's the way the players are talking in there. It was a bad one."
However, it is understood the Football Association (FA) will not take action against Ferguson as he did not suggest Atkinson was biased or question the referee's integrity.
English champions United are now five points behind league leaders Chelsea.
Ferguson was charged last month with improper conduct by the FA for publicly labelling referee Alan Wiley "unfit" after United's 2-2 draw with Sunderland.
The 67-year-old Scottish manager later apologised by saying: "I apologise to Mr Wiley for any personal embarrassment my comments may have caused and to the FA for going public with my views.
"In retrospect I accept that they could be deemed as expressing those views in an inappropriate form."
Officials have yet to decide what action, if any, to take regarding Ferguson's comments about Wiley