The England forward acrobatically volleyed home Nani's 77th-minute cross to take United eight points clear of City in the league standings en route to a record 19th English league title, and the award is the first in a series to commemorate 20 seasons of the Premier League.
Hundreds of thousands of supporters across the globe voted in the poll, with Rooney's strike gaining 26% of the total votes cast. Dennis Bergkamp's sublime turn and finish against Newcastle for Arsenal in March 2002 was the second most popular with 19%, and Thierry Henry's volley for Arsenal against Manchester United in 2000 was third on 15%.
Rooney said: "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.
"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."
Over 4.2million votes were cast by 300,000 supporters to decide the best goal, best save, best goal celebration and a fans' fantasy team. There are also six award categories being decided by a panel - best player, manager, team, season, most memorable quotes and a panel fantasy team.
The remaining award winners will be named over the next fortnight culminating in an event on May 15 where the best player and manager of the 20 seasons will be revealed.
The 20th Premier League season has featured some fantastic goals, with Wednesday's swerving strike from Newcastle striker Papiss Cisse against Chelsea arguably the pick of the 2011-12 campaign so far, coming just days after Luis Suarez's long-range chip for Liverpool against Norwich.
Source: PA
Source: PA