RooneyÃ¢â‚¬â„¢s 78th-minute strike helped United, who were looking to bounce back after their shock defeat at Wolves last week, temporarily move seven points clear of Arsenal at the top of the Premier League table.
The result effectively also ends City’s title ambitions as they now find themselves eight points behind their neighbors having played a game more.
Nani opened the scoring for the home side five minutes before the break, but the visitors drew level through David Silva’s 65th-minute deflected equaliser before Rooney netted his fifth league goal of the season in style.
The visitors started the game well and should have taken the lead inside three minutes. Silva, Carlos TÃƒÂ©vez and Yaya TourÃƒÂ© combined well down UnitedÃ¢â‚¬â„¢s left-hand side and the Spaniard raced through on goal only to poke his effort wide of the far post from five yards out.
Roberto Mancini’s men dominated much of the first half and it took United until the 33rd minute to trouble Joe Hart in the City goal. Darren Fletcher rose above Pablo Zabelata at the back post to meet a Ryan Giggs cross, but his header was smothered well by the England goalkeeper.
United, who started poorly and struggled to find their usual rhythm, took the lead against the run of play when Rooney headed on a Edwin Van der Sar goal-kick to Ryan Giggs, whose first time ball was controlled and put away by Nani.
At full stretch the Portuguese winger brought down GiggsÃ¢â‚¬â„¢ ball and accelerated away from the chasing Pablo Zabaleta before calmly slotting the ball past Hart.
The second half started as the first ended with neither team able to gain full control of the game or fashion any real goal scoring opportunities, despite some good approach play.
Former United front man TÃƒÂ©vez and Silva were behind much of CityÃ¢â‚¬â„¢s attacking efforts and were ably assisted by substitute Shawn Wright-Phillips, who was not afraid to run at the home side’s defence – and it was his attacking intent that created CityÃ¢â‚¬â„¢s equaliser.
The winger took on Patrica Evra and his cross was met by fellow substitute Edin Dzeko whose shot deflected off the back of Silva and past Van der Sar in 64th minute.
Sir Alex Ferguson reacted to seeing his side pegged back by sending on the Premier LeagueÃ¢â‚¬â„¢s top scorer Dimitar Berbatov, but it was Rooney who stole the headlines.
NaniÃ¢â‚¬â„¢s deflected cross looped up in the air and Rooney met it in mid air with an acrobatic overhead effort which rocketed past EnglandÃ¢â‚¬â„¢s number one Hart, who was left rooted to the spot.
Rooney later hailed the strike as the best of his career. “As soon as I hit it, I knew it was in and it’s definitely the best goal I’ve scored,” said the England forward.
“It was a special feeling. The fans deserve that from me because I’ve not had the best of seasons.”
And United boss Ferguson led the praise for Rooney’s winner after the final whistle. “It was stunning,” said Ferguson. “Unbelievable. We’ve had some fantastic goals here but in terms of execution, you’ll never see that.”
Ferguson’s league leaders stay four points clear of Arsenal after the gunners cruised to a 2-0 victory over Wolves at Emirates Stadium thanks to a Robin van Persie brace.
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