The tearful 28-year-old Real Madrid and Portugal star had been the overwhelming favourite to pip Barcelona and Argentina star Messi, winner the previous four years, and France's Franck Ribery, who won the treble with Bayern Munich in 2013.
"Thank you to everyone, my team mates, the national team and my family, to everyone her, an emotional Ronaldo said at the awards.
Named after former US President Ronald Regan, Ronaldo remembered Portugal great Eusebio and former South African president Nelson Mandela in his acceptance speech.
“Eusebio and Mandela were very important for me, I can't speak."
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.
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