Although he failed to win any major titles with Real Madrid last season, Ronaldo was rewarded for his immense goal-scoring prowess as he swept aside Messi, winner for the last four years, and Frenchman Franck Ribery.
"Thank you to everyone, my team mates, the national team and my family, to everyone here," the Portugal and Real Madrid forward said, choking with emotion after accepting the trophy.
"I can't speak," added Ronaldo, runner-up for three of the last four years, before breaking down.
Jupp Heynckes, now retired, was named coach of the year for the first time after leading Bayern Munich to an unprecedented Bundesliga, Cup and Champions League treble, a fitting end to a 48-year career as player and coach.
The Afghanistan Football Federation and fiery Sweden striker Zlatan Ibrahimovic were among other award winners.
Afghanistan was given the Fair Play award after staging its first home game for 10 years, a friendly against Pakistan.
Ibrahimovic won the Ferenc Puskas award for the best goal of the year, although his stunning overhead kick from near the touchline in a friendly against England was scored in 2012 and missed the deadline for last year's ceremony.
The volatile Swede, who in November said that he did not need the Ballon d'Or to know he was the best, was surprisingly mild in his acceptance speech, limiting himself to thanking the audience and wishing good luck to the contenders.
The ceremony, hosted by former Netherlands international Ruud Gullit and Brazilian presenter Fernanda Lima, took nearly 90 minutes, interrupted by banal interludes featuring personalities from 2014 World Cup hosts Brazil.
Brazil forward Neymar, among those to be hauled on stage, was clearly embarrassed when asked to say who he would like his team to meet in the World Cup final.
"We don't care, we will meet anybody. There are so many other great teams there, as long as we are in the final I don't mind," he said timidly.
Voting was in the hands of the 209 national team coaches and captains, plus 173 selected journalists, and FIFA was at pains to point out that the process was transparent, especially after the original deadline was extended by two weeks due to a poor turnout.
FIFA spokesman Walter De Gregorio said the deadline extension, from Nov. 15 to Nov. 29, had not affected the outcome which was independently audited by accounting firm Price WaterhouseCoopers (PWC).
"The ranking of the final three at the end of November is exactly the same as the ranking in mid-November," De Gregorio told reporters. "The only difference is that we had more votes."
The poll for both player and coach of the year leaned heavily towards Europe.
Ivory Coast and Manchester City midfielder Yaya Toure was the only African player to make either of the original shortlists of 23 players and 10 coaches and there were no representatives from Asia or CONCACAF.
Brazil's Luiz Felipe Scolari was the only South American coach to be considered. Stephen Keshi, who won the African Nations Cup with Nigeria, and Safet Susic, who led Bosnia to their first World Cup, were among those to be overlooked.
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