United suffered their second Premier League defeat of the season at Stamford Bridge.
Rooney gave United the lead, but it was cancelled out by David Luiz and Frank Lampard’s penalty.
Ferguson felt the spot-kick was a soft one.
“I think that we defended badly on the first goal, that was a bad one to lose, but the penalty kick was so soft,” Ferguson told Sky Sports.
“We played very well and I thought it was a great performance by us, we didn’t deserve that and that’s three years in a row that referees’ decisions have changed the game.”
Ferguson was also unhappy that David Luiz escaped a red card.
Ferguson said: “It’s incredible. Even before that, he’s done Chicharito off the ball, he’s done him late and there’s nothing done and the referee’s in front of it.
“Then he does Rooney, it’s clear as day and he’s six yards from it, but he doesn’t do anything – that changes the game.
“You’re talking about what changed the game in the second half and these decisions changed the game, and he’s going to be refereeing every week.”
The United boss added: “With decisions like tonight, it can change anything. They got a lot of decisions tonight and that surprised me in a major game like that, I’m surprised.”