Furious Fergie lashed out after Frank Lampard's late penalty shot down United and blew the title race wide open again.
Just three days after Wayne Rooney's elbow storm at Wigan, Ferguson claimed Atkinson should have sent off Blues' goal hero David Luiz for clattering the England striker.
And to make it worse, Nemanja Vidic was red-carded in injury time Fergie rapped: "It was a major game, you want a fair referee and we didn't get that.
"I don't know why he got the game. I feared the worst when I saw who was refereeing.
"It's three years in a row now where the referee's decisions have changed the game down here. And that's hard to take."
Luiz cancelled out Rooney's first-half goal but it was the defender's off-the-ball trip on his star striker which enraged Ferguson.
He added: "Six yards in front of the ref, maybe eight yet he gives him the benefit of the doubt.
"It was incredible. Even before that, he'd done Chicharito off the ball.
"I don't know how Luiz stayed on the pitch."
FA chiefs are bound to take a dim view of Ferguson's blast especially in the wake of the leniency shown to Rooney after he elbowed Wigan's James McCarthy last weekend.
Vidic was sent off for a second yellow card in injury time and the United skipper is now banned for Sunday's crunch trip to Liverpool.
Lampard - watched by girlfriend Christine Bleakley and pal Geri Halliwell - struck 11 minutes from time after Chris Smalling fouled Yuri Zhirkov.
But Fergie insisted: "The penalty was so soft. It was a great performance from us and we didn't deserve that."
Chelsea moved back into the top four, 12 points behind United with a game in hand.
And boss Carlo Ancelotti insists Ashley Cole's airgun incident at the club's training ground has not affected his squad.
The Italian said: "I spoke an hour about Ashley yesterday. He played a good game.
"We never had a problem with the unity of the players. They are always together, in good and bad moments. This victory is important for us and our confidence."
Home game always get some sort of advantage...but anyway Chelsea has yet to go to Old Trafford, isnt it???