United ultimately fell short in their bid to win a fourth successive Premier League title, beaten by a single point as Chelsea romped home against Wigan Athletic on the final day.
Rooney was also beaten out by Blues hitman Didier Drogba for the league's top goalscorer award, as the Ivorian grabbed a hat-trick against the Latics to edge their individual race with 29 strikes to his name.
But Rooney was nonetheless the choice of the awards panel, which includes representatives from football's governing bodies, the media and fans, after leading Sir Alex Ferguson's side from the front for the majority of the season.
Rooney notched his 26 goals in 32 games for the club, after injuries affected the conclusion of his campaign. The total easily beat his previous best mark of 16.
Rooney's award follows after Tottenham Hotspur manager Harry Redknapp was named manager of the season. Redknapp guided the north London club to an impressive fourth place finish, securing Champions League qualification for next season.
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