Argentine Messi, hampered by uncharacteristic injury problems at Barcelona late in the year, and Frenchman Franck Ribery of Bayern Munich were the other candidates for the prize, officially known as the FIFA Ballon d'Or.
Jupp Heynckes, now retired, was named coach of the year for the first time after his Bayern Munich team won an unprecedented Champions League, Bundesliga and German Cup treble.
Ronaldo was also voted FIFA Player of the Year in 2008, before Messi began a run of four successive titles.
In 2010 and 2011, the award was fused with the Ballon D'Or award previously handed out by France Football magazine.
Although Ronaldo did not win any major titles last season, he has been unable to stop scoring goals.
The 28-year-old has 20 La Liga goals this season for Real Madrid and netted a record nine times in the Champions League group stage.
The high point of his year, however, came with Portugal when he scored a stunning hat-trick and almost single-handedly beat Sweden 3-1 in the second leg of their World Cup playoff tie to send his country through to the finals.
The team of the year featured Manuel Neuer in goal, Philipp Lahm, Sergio Ramos, Thiago Silva and Dani Alves in defence, midfielders Andres Iniesta, Xavi and Ribery with Ronaldo, Zlatan Ibrahimovic and Messi in attack.
(Editing by Ed Osmond) nL6N0KN3BG
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