Rooney's selection ahead of Cesc Fabregas, Carlos Tevez and Didier Drogba means United have supplied the winner of the award for a fourth successive year.
The 24-year-old has been in sensational form this season, scoring 34 goals for United and eight for England, and is key to the nation's World Cup hopes.
"It's a great feeling to win the player of the year award because it's voted for by the players," said Rooney.
"It's something I'm really proud of and it's a great honour.
"I remember coming here in 2005 and 2006 to win the young player of the year.
"I saw the players winning the main one and it's something I've aimed for since."
Rooney, who has only just returned from an ankle problem, missed the weekend's 3-1 victory over Tottenham with a groin injury sustained in training.
The Premier League's top scorer with 26 strikes hopes to return for United's campaign finale against Stoke next month and promised he will be fit for the World Cup.
"The groin will be fine for the World Cup, there are no worries about that,2 he said.
"I'm hoping to play for United in the last game of the season."
Rooney, the first Englishman to win the award since Steven Gerrard in 2006, paid tribute to the influence United manager Sir Alex Ferguson has had on his career.
"Sir Alex is a great manager who has really brought me on as a player since I joined United," he said.
"His hunger passes through to the players. It's great to see that he's pushing 70 and hasn't changed a bit.
"I'm sure he'll be here for a long time yet."
Rooney was also nominated for the PFA Young Player of the Year, but that award went to Milner.
Milner appears to have played himself into Fabio Capello's World Cup squad with a string of stellar performances and the 24-year-old midfielder credited a change in position for his success this season.
"I've been moved into the middle and that suits me as it helps me influence the game a bit more," said Milner.
"Maybe sometimes wide right you want to influence the game but you just can't get yourself into it."
Leeds legend and former South Africa captain Lucas Radebe, 41, won the PFA Merit award.
"I'm very proud to get such a great award. Sport can change the world - football has played such a big part in lifting my community," said Radebe.
The PFA divisional team of the year contains four United players, spearheaded by Rooney.
Arsenal, whose title challenge fell away in the final rounds, supply Fabregas and Thomas Vermaelen and there are also two from Chelsea in Drogba and Branislav Ivanovic.
The inclusion of Milner and Richard Dunne means Aston Villa are represented twice as well.
Premier League team of the year: Hart, Ivanovic, Vermaelen, Dunne, Evra, Fabregas, Milner, Fletcher, Valencia, Rooney, Drogba.