The tearful 28-year-old Real Madrid and Portugal star, who won the award in 2008, had been the overwhelming favourite to pip Barcelona and Argentina wonder Messi, winner the previous four years, and France's Franck Ribery, who claimed the treble with Bayern Munich in 2013.
Ronaldo won with 27.99% of the votes ahead of Messi (24.72%) while Ribery was third (23.36%) according to France Football, co-organisers of the award with FIFA.
"There are no words to describe how I feel," said Ronaldo.
"I'm delighted, I want to thank all my team-mates, all my family in the room.
"Those who know me know how many sacrifices I made to win this reward.
"I want to thank all those who had faith in me and I want to speak again about (recently deceased Portugal legend) Eusebio and (recently deceased former South Africa president) Madiba (Nelson Mandela) and to pay tribute to them one last time."
"Without doubt I deserved this, Messi and Ribery would have also deserved it.
"Each time is different. But I would say that this second Ballon d'Or is more emotional, because my mother and my son (who joined him on stage) are here."
Real president Florentino Perez paid tribute to Ronaldo.
"The only thing I wish to say is that this Ballon d'Or is justified to be for Cristiano Ronaldo, it is recognition of hard work, talent, and a desire to win daily."
For Messi, sporting a striking red dinner jacket, Ronaldo's win didn't change very much.
"I would have loved to have won, but as it is the motivation is the same to keep growing, improving and winning things," he commented via Barcelona's twitter page.
However, UEFA President and French football icon Michel Platini found it strange that Ribery should miss out in a year that he helped Bayern carry all before them.
Indeed Platini, who won the Ballon d'Or three times, said the nature of the award had changed since it fell under FIFA's aegis in 2010.
"I am very disappointed for Franck Ribery. Next year we will return and it will be Messi-Ronaldo, in two years time the same and three years time ditto.
"I am disappointed because for 50 years the Ballon d'Or took into account results and trophies on the pitch.
"Here we are talking about the global value of players and that poses a problem."
Ronaldo, who was widely expected to win after news spread on social media earlier in the day seven members of his family were joining him in Zurich and his club Real were transmitting the award ceremony live on their official television channel in a change to the programmed schedule, broke down in tears on stage during his victory speech.
Ribery, who won the Champions League, Bundesliga and German Cup with Bayern last season, before adding the European Supercup and Club World Cup before the turn of the year, had been the early front-runner.
But a controversial two-week extension to the voting deadline for international coaches, captains and media meant those casting their ballots could take into consideration Ronaldo's remarkable hat-trick to beat Sweden in the World Cup play-offs in November.
That was widely believed to have been enough to tip the scales in his favour.
However, with 66 goals in his 56 matches this year — more than Messi and Ribery's combined 65 — no-one could deny Ronaldo was a worthy winner.
It is the second time he has picked up the award and comes in a season in which he won nothing with either club or country, an unusual situation for a Ballon d'Or winner.
As expected, Bayern's Jupp Heynckes, who retired following their historic treble in May, won the coach's award.
German goalkeeper Nadine Angerer was named women's Ballon d'Or winner while Germany coach Silvia Neid won the women's coach award.
A special honorary Ballon d'Or was given to Brazilian legend Pelé, who never qualified for the award during his playing career as he never plied his trade in European club football.
From its inception in 1956 until 2010, the Ballon d'Or was awarded to the best player in Europe and the FIFA World Player of the Year award was only inaugurated in 1991, before ending in 2009 when it was assimilated into the Ballon d'Or.
Zlatan Ibrahimovic won the Ferenc Puskas best goal award for his stunning, acrobatic overhead kick from 40 yards for Sweden in a friendly against England.
Former IOC president Jacques Rogge was given the president's prize for a "remarkable personality in sport".