Rooney went into the tie still not knowing what his punishment will be for the four-letter outburst at West Ham on Saturday.
But the uncertainty didn’t affect him as he took full advantage of a superb piece of skill by Ryan Giggs to give United their first win at Stamford Bridge in 2002 and put them in pole position to reach the semi-final at Old Trafford next week.
Chelsea are not out of it. Indeed, a repeat of the 2-1 success on their last trip to Old Trafford 12 months ago will be enough to send through.
However, they will have to do far better in front of goal – and £50million man Fernando Torres in particular must start scoring after yet another ineffective display ended with an injury-time yellow card for diving.
At Upton Park on Saturday, Rooney completed his hat-trick, then headed straight towards a TV camera to deliver his ill-advised reaction that threatens his place in the FA Cup semi-final with Manchester City.
As his first-time effort caressed the base of Petr Cech’s left-hand post and rolled gently into the back of the Chelsea net, he again ran towards the lens.
This time, he stopped short, slid to his knees and waited to be mobbed by ecstatic team-mates.
They had every right too, especially Ryan Giggs given his outrageous contribution.
Now 37, Ferguson has claimed the veteran Welshman could go on for a couple of years yet. How the United boss must hope that is true.
Having watched Michael Carrick deliver a pinpoint crossfield pass that was sensational in itself, Ferguson could only sit back and admire Giggs’ sublime first touch, which took him careering past the stranded Jose Bosingwa, and the coolness of his second, which left Rooney with a tap-in.
Cue delirium amongst the United contingent, satisfaction for Rooney and the precious away goal Ferguson had demanded.
Carlo Ancelotti could only urge his team – who had started the brighter – into some kind of response.
It should have come in the final minute of that opening period.
Didier Drogba went for goal from an acute angle but his shot lacked power.
Torres closed in, yet somehow completely missed the ball from a central position on the edge of the six-yard area.
As the ball bounced back off the post, Frank Lampard went to tap home, only for Patrice Evra to clear off the line.
Given Saturday’s draw at Stoke and Inter Milan’s stunning demise to Schalke in the San Siro last night, it is hardly overestimating the situation to say Carlo Ancelotti’s job hangs on reaching the final, and for that Torres needs to do what Roman Abramovich paid all that money for.
United suffered a hammer blow within minutes of the restart when Rafael went down after a seemingly innocuous tangle with Drogba.
The young Brazilian bravely tried to continue but the pain in his left knee made it impossible, the stretcher carrying him away for what looks like a lengthy period.
Ferguson’s response was typical. With no obvious right-back replacement, instead of introducing a defender, in Chris Smalling or Jonny Evans, he went for Nani, asking Antonio Valencia to plug the gap.
Chelsea were able to get up a head of steam though.
Ramires wasted an excellent chance when he glanced Drogba’s effort wide of the far post.
The Ivorian himself was not too far away with a speculative overhead kick.
United’s defence – which has not conceded an away goal in this competition this season – held firm and came agonisingly close to grabbing a second when Nani drilled a cross to the far post that would have allowed Javier Hernandez to head into an empty net had Cech not gambled in a desperate attempt to claw the ball away from the Mexican.
The departure of Drogba for Nicolas Anelka 20 minutes from time placed even more weight on Torres’ shoulders just after Michael Essien had gone close for the hosts.
And the Liverpool man so nearly responded when he rose to meet Jose Bosingwa’s far-post cross and sent a header curling towards the corner that Van der Sar, troubled by a groin problem, was at full stretch to claw away.
United then breathed a sigh of relief in stoppage time when Patrice Evra sent Ramires tumbling but referee Alberto Mallenco failed to award what seemed to be a clear penalty.
There was still time for a Torres yellow card for diving under Valencia’s challenge, ending yet another unhappy night for the Spain star.