After dragging United back on level terms against AC Milan with an instinctive second-half strike from Paul Scholes' inspired pass, Rooney then latched on to a Ryan Giggs through ball before lashing home a phenomenal first-time effort which sealed a 3-2 first-leg win.
Providing they avoid defeat in the San Siro next Wednesday, they will confirm an all-English meeting with either Chelsea or Liverpool in Athens on May 23.
And Ferguson knows who he will have to thank.
"Wayne was a threat to Milan all night," said the United boss.
"We played him up front on his own because we wanted to stretch their defence.
"It meant he wasn't going to get the greatest involvement in the match but he still made some fantastic runs between the two central defenders and of course, the winning goal was an incredible hit.
"He didn't take a touch on it, just hit it first-time. It was a brilliant goal.
"On an occasion like tonight, we needed our big players to hit the heights."
The victory was all the more remarkable given it was achieved without six key players, including three-quarters of Ferguson's first-choice defence.
Cristiano Ronaldo gave the hosts a perfect start when he met Giggs' corner with such power Dida was unable to keep it out despite two attempts.
At that stage, another handsome win appeared to be on the cards, only for Milan's own boy-wonder, brilliant Brazilian Kaka, to turn the game on its head with a well-taken double which exposed United's defensive frailties.
For a time, it seemed the hosts would be swept away. But somehow they clung on and, thanks to Rooney, head to Italy with a precious lead.
"I don't think anyone expected us to fold when we fell behind," said Ferguson.
"We have an outstanding chance now because, with the speed of our game, I believe we will score in Italy. Whether it will be enough I don't know.
"It will not be easy - but it will not be easy for them either."
The one regret for United is the booking Patrice Evra picked up which will rule him out of next week's decider.
However, Milan coach Carlo Ancelotti has problems too with Paolo Maldini almost certainly out as well with a knee injury and influential midfielder Gennaro Gattuso facing a race against time to recover from a toe problem which forced him off midway through the second-half.
"Manchester United probably do have a slight advantage," conceded Ancelotti.
"We are disappointed about their winning goal because I felt we had the match pretty much in hand.
"It seemed we were going to get a good result but that goal has complicated matters."