The Red Devils bounce back after going behind early as the England international strikes for the first time this season while Robin van Persie and Danny Welbeck also find the net
The visitors took the lead when the England international nodded the ball into his own net from a Charlie Adam free-kick. United rallied and Rooney was on hand to get them back into the game with a thumping header.
Just before the break Robin van Persie gave his side the lead with sublime close range effort and 50 seconds after the restart Danny Welbeck notched another for the Red Devils with a superb diving header.
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Sir Alex Ferguson made two changes to the side that beat Newcastle with Antonio Valencia and Paul Scholes coming in for Shinji Kagawa and Tom Cleverley. Tony Pulis made just one change from his Potters team that drew with Liverpool with Dean Whitehead replacing Glenn Whelan.
The Red Devils dominated possession early on but it was the Potters who took the lead through an own goal from Rooney who could only helplessly nod Adam’s free-kick past David De Gea when trying to mark Shawcross.
Every time Stoke pushed forward they threatened and De Gea had to make two good saves to stop the visitors doubling their lead, first from Adam, and then from Walters after Kightly and Peter Crouch had combined to set the striker one-on-one with the Spaniard.
The Potters were made to rue these missed opportunities as United equalised through Rooneyas he rose highest in the penalty area to head Van Persie’s cross into the right net this time for his first league goal of the season.
United upped the ante before the break as Scholes and Welbeck went close before they took the lead through Van Persie as he turned Valencia’s pinpoint cross past Begovic at the near post with a lovely finish taking the ball first time with his left-foot.
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The Potters had shown earlier they were not going to be pushovers and they regained that attitude as they equalised through Kightly with a great individual effort as he ran through the United defence and shot past De Gea with the aid of the post.
Stoke’s hopes of getting back into the game further were dented when Rooney struck again from close range as he reacted first to a scramble in the penalty area from a Van Persie corner and side-footed into the net at the back-post.
The Potters tried desperately to fight their way back into the game again while United had chances of their own to extend their lead but neither could find a way through again as Sir Alex’s side sealed the three points.