Premier League - Was Fergie's fury justified?
Did the referee get it wrong? Watch the video and judge for yourself - autoplay in UK only
United had centre back Nemanja Vidic sent off in stoppage time for a second booking but Ferguson was incensed that David Luiz had not suffered the same fate earlier and was also unhappy with the penalty given after Chris Smalling tripped Yuri Zhirkov.
"The penalty kick was so soft but we played very well. It was a great performance by us. We didn't deserve that," said Ferguson.
"That's three years in a row referees' decisions have changed the game (here)."
Luiz was booked by referee Martin Atkinson for a foul after 61 minutes then appeared fortunate to escape a second yellow card after flattening Rooney.
"It was incredible. Even before that he'd done Chicharito (Javier Hernandez) off the ball. He'd done him late. Nothing done, the referee's in front of it," added Ferguson.
"He (Luiz) does Rooney clear as day, he's six yards from it, he doesn't do anything. These are decisions that change the game and he's going to be refereeing every week."
Ferguson, who said before the game that Rooney was lucky not to have been banned after a clash with Wigan Athletic's James McCarthy at the weekend, added: "I'm proud of the players. They've endured a lot of decisions against them but they've come through it, they've done their best and created good chances."
Chelsea's win took them within 12 points of leaders United and, asked if they were back in the title race, Ferguson said: "If they get decisions like tonight then it can change everything. They got a lot of decisions that surprised me."
Chelsea boss Carlo Ancelotti did not want to discuss the officials but said Luiz might have been lucky.
"There was a lot of intensity and it was not easy for the referee to decide every time," he said. "There was a lot going on on the pitch so the referee decided he didn't see this."
The Italian preferred to concentrate on the spirit shown by his side after they had been outplayed in the first half.
"We kept going with strength, intensity and power in our performance against a fantastic United team," he said.
"We actually started well but at halftime I told them that we had to do it for 45 minutes, not just 15.
"It was not easy to come back but we had a good balance in the second half."
The win took Chelsea back into the top four but Ancelotti said the champions had no realistic hope of catching United, who are four points ahead of Arsenal having played a game more.
"It's too far, we can't think we can get to the top," he said. "But the victory was important for us and our confidence."
Midfielder Lampard added: "We're still a lot of points behind but all we could do was win the game.
"United are deservedly top but we've still got some fight in us and we showed that tonight."