England striker Rooney 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.
Supporters from around the world voted in the ballot, with Rooney's effort gaining 26 percent of the total votes cast.
Dennis Bergkamp's magnificent turn and finish against Newcastle for Arsenal in March 2002 was the second most popular with 19 percent and Thierry Henry's volley for Arsenal against Manchester United in 2000 was third on 15 percent.
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."
The current Premier League season, which has two games left to run, has produced several goals that could be remembered as long as Rooney's award-winning effort, notably Newcastle striker Papiss Cisse's astonishing swerving strike from the touchline in a 2-0 win away to Chelsea on Wednesday.