Former Red Devils winger Keith Gillespie had stunned the visitors by scoring his first goal for the Blades on his 44th appearance.
But the visitors, and Rooney especially, were not to be denied as the striker made it three goals in four days after finding the net in England's 1-1 draw in Holland in midweek.
On this occasion, Rooney was allowed two opportunities, and he finished both with cool aplomb to take his tally to seven for his club and eight overall for the season.
Sir Alex Ferguson's side should perhaps have finished with more than Rooney's double to show for their dominance, but it was one of those wayward days in front of the net.
The visitors should have taken the lead in the 10th minute after Colin Kazim-Richards, the goalscoring hero of last week's 2-2 draw with Bolton, made a hash of intercepting Cristiano Ronaldo's ball wide to the right.
Poor control allowed skipper Gary Neville to steal in, charge into the area and drive in a right-foot shot that was saved by the legs of Paddy Kenny.
It proved a let-off and three minutes later the Blades made their illustrious visitors pay by taking the lead, with Rio Ferdinand's mistake the root cause.
Under pressure from Kazim-Richards, Ferdinand aimlessly hacked the ball down the touchline, only for rookie midfielder Nicky Law - on his full debut - to intercept.
A cushioned header to Kazim-Richards, followed by a return pass, afforded the 18-year-old time and space to deliver a raking cross from the left wing.
Surprisingly unmarked at the far post it gave Gillespie a moment to savour as he headed the opener from an awkward angle across Edwin van der Sar from eight yards.
The majority of a season-high crowd of 32,584 were still pinching themselves when the visitors came close to an instant riposte.
But Kenny - declared mentally fit to start despite much-publicised marriage difficulties and sporting a large plaster over his left eyebrow, which was bitten off in a brawl earlier this week - made another superb save.
This time the Republic of Ireland international was full stretch in tipping away a flick header from Rooney as the England international had risen to meet a right-wing ball from Ronaldo.
Then controversy followed in the 26th minute when Ferguson's side were denied the first of two strong penalty shouts in the opening 45 minutes.
Rooney's clipped through ball for Louis Saha led to the Frenchman receiving a barge in his back from Rob Kozluk.
Despite a clear view of the incident, referee Mark Clattenburg waved away appeals and was immediately surrounded by four angry Manchester United players.
Standing for no nonsense, an unrepentant Clattenburg booked Ryan Giggs, who perhaps had cause to feel aggrieved as it was one of those decisions that has been given in the past.
At that stage, though, the Red Devils were in full control and their reward arrived on the half hour.
Neville's low curled ball into the heart of the area from the right was picked up by Rooney, who had got between covering defenders Claude Davis and captain Phil Jagielka.
After an initial controlling touch with his left foot, Rooney then fired the equaliser past Kenny with his right from six yards.
Just before the interval, United were fuming again as Clattenburg turned away another penalty shout - albeit less obvious - after Paul Scholes was challenged from behind by Alan Quinn just before the interval.
Come the half-time whistle, and as the players made their way off the pitch, an unhappy Giggs aired his views to Clattenburg.
Fortunately, the official enjoyed a quieter second half in which all the action was confined to the closing 15 minutes, and after the Blades' spirit had been broken by Rooney's second.
Patrice Evra's left-wing cross just evaded the head of Davis, and lurking behind was Rooney to volley home from eight yards.
Ronaldo then hit the bar, Scholes saw his rebound cleared off the line by Jagielka, while Saha saw a 20-yard drive superbly saved by Kenny.
That was all before one of those glaring misses that will probably be replayed time and again - on this occasion Ronaldo spooning the ball over an empty net from four yards after being teed up by Giggs.
Fortunately, it did not prove costly for Ferguson and Rooney.