Barcelona's Argentine forward Lionel Messi was second, with Liverpool and Spain striker Fernando Torres third.
Spain midfielder Xavi Hernandez, also of Barcelona, and AC Milan's Brazilian playmaker Kaka completed the top five.
Ronaldo won the honour for the first time after helping United win the Premier League, Champions League and Club World Cup.
It also completed a hat-trick of individual honours for the 23-year-old, who had already won the football journalists' Ballon d'Or trophy and the FIFPro World Player of the Year title voted for by his fellow professionals.
"It's an overwhelming moment, very special," said Ronaldo after receiving the FIFA award from Pele.
"I can say to my mother and sister, 'let the fireworks off now'. It's one of the most important moments in my life."
ENGLISH FIRST
Ronaldo is the first player based at an English club to win the FIFA award, which had previously gone only to footballers playing for Spanish or Italian sides.
"There may be no English players here but I believe it's important for England that myself and Fernando Torres are here representing two English clubs," said Ronaldo before the ceremony.
"It is a victory for the English fans as well because the Premier League is strong, even though we must not forget the leagues in Spain and Italy remain strong as well."
The FIFA award is voted by the national team coaches and captains of the 208-member associations of world soccer's governing body.
Ronaldo was voted in first place by 136 of the coaches and captains while 76 put Messi top.
The United player picked up 935 total points, ahead of 678 for Messi and 203 for Torres.
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