Ronaldo was crowned the best player in the world once before, back in 2008 while at Manchester United, but since then he has had to play second-fiddle to Messi in the voting, finishing runner-up three times as the Barcelona ace claimed the title on a record four successive occasions.
However, the Real Madrid star was back on top on Monday night after being named as the 2013 Ballon d'Or winner at an awards ceremony in Zurich.
The 28-year-old, who did not win any silverware with Madrid last year but scored a remarkable 69 goals for club and country, secured 1,365 points in the voting, with Messi having to settle for second place with 1,205 and Bayern Munich winger Franck Ribery third with 1,127.
An emotional Ronaldo paid tribute to his team-mates and family for helping him win the award, and hopes to be back in the same position in 12 month's time.
He said: "I have no words to describe this moment. Thanks to all of my team-mates, at Real Madrid and the national team.
"Without all of their efforts this would not have been possible. I am very happy, it is very difficult to win this award.
"Everybody that has been involved with me on a personal level I have to thank. My partner, my friends, my son. It is a tremendously emotional moment."
Ronaldo, who has scored 231 goals in 222 games for Madrid since joining them from United in 2009 and last week passed 400 goals for his career, added on www.fifa.com: "I'm going to try to give my best, like I always do, and I hope to be back next year to win the third Ballon d'Or of my career. That's what I intend to do."
Despite being hit by injuries, Messi also had another memorable year in 2013, although it was not quite enough to see him claim a fifth successive award and he hailed Ronaldo as a just winner.
"I want to congratulate Cristiano because he was the winner and deservedly so," said the 26-year-old, who was also asked if things might have been different if he had been fully fit for the whole year.
"I don't know if without the injury it would've been different. I was out for a lot of time, that's true. But that's neither here nor there. Cristiano merits it," he said in AS.
In some of the other awards, Germany goalkeeper Nadine Angerer won the women's top prize for the first time while Jupp Heynckes was named men's FIFA World Coach of the Year.
Heynckes led Bayern to a record-breaking treble of Champions League, Bundesliga and German Cup in the 2012/13 campaign before stepping down at the end of the season. In the voting he collected more than double the points of second-placed Jurgen Klopp, the Borussia Dortmund manager, with former Manchester United boss Sir Alex Ferguson finishing in third spot.