Several hundred thousand fans from all over the world voted for the award, which was created to celebrate the 20th season of the Premier League.
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“I grew up watching the Premier League so to be voted the best goal in the history of the Premier League is a great feeling”
Rooney's spectacular strike in February 2011 received 26% of the vote.
Dennis Bergkamp was second for his 2002 goal at Newcastle, and Thierry Henry against Manchester United was third.
Bergkamp's flick, turn and finish at St James' Park polled 19% of the vote and Henry recorded 15% for his flick and volley at Highbury in 2000, but Rooney was crowned champion for his acrobatic effort in the Manchester derby at Old Trafford.
He follows another Manchester United player, David Beckham, who won the Goal of the 10 Seasons Award in 2002 for his audacious strike from the halfway line against Wimbledon.
"I grew up watching the Premier League so to be voted the best goal in the history of the Premier League is a great feeling," Rooney said.
"There's so many good goals in that shortlist, goals that I watched in my living room as a kid: Alan Shearer's goal, Paolo Di Canio's, Tony Yeboah's, David Beckham's.
"To be competing with them and winning is a great honour for me and something I'm very proud of. I'd like to say a big thank you to all the fans that voted for me."