Ronaldo has won the award 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 Argentinian claimed the crown on four successive occasions.
That is despite the Portugal international putting up incredible figures for Real Madrid - he has scored 231 goals in 222 games for the Spanish giants - which at any other time would surely have been enough to win a host of gongs, as Messi has.
The problem for Ronaldo has been that Messi, and his club Barcelona, have been in record-breaking form in recent years and few could deny the Argentinian ace deserved his place as the game's leading light.
No more, though.
Ronaldo was on Monday night awarded with the 2013 FIFA Ballon d'Or at a ceremony in Zurich after securing 1,365 points in the voting, with Messi having to settle for second place with 1,205 and France international Franck Ribery third with 1,127.
Ronaldo did not win any silverware with Madrid last year but he was in phenomenal goalscoring form, netting 69 times for club and country, including all four goals in Portugal's 4-2 aggregate victory over Sweden in the World Cup qualifying play-offs.
In accepting the award, a teary and humble Ronaldo was quick to highlight the support of his team-mates.
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. All I can say is thank you to everybody that has been involved."
In the mixed zone afterwards, the Portugal captain was quoted as saying by AS: "I don't know if it's fair or not. Ribery could have won it as much as me.
"I've had a very good season at an individual level. I want to be here again next year and win it again.
"My mum (who was in attendance) cries very easily and when I saw her crying it made me cry as well. I'm an emotional person."
On his rivalry with Messi, the 28-year-old added: "I have a very professional relationship with Messi, he's a player I admire. I'm happy to compete with the best. I'm going to try win things with Madrid and the national team, and I hope to be here (again next year) and win."
Messi had held exclusive rights to the award in recent seasons as he became the first player to win the Ballon d'Or four consecutive times.
He too had another memorable year in 2013, but it was not quite enough to see him claim a fifth successive gong and he hailed Ronaldo as a just winner.
"I want to congratulate Cristiano because he was the winner and deservedly so. I think it was a good year for the three of us and that's why we were there. I have nothing to complain about or make any excuses," said the 26-year-old, who again caught the attention at the gala with his fashion choice as he wore a shiny burgundy three-piece suit.
Just behind the duo in the voting - made by national team coaches and captains plus members of the international media - was Ribery, who finished in the top three for the first time.
The Frenchman's efforts helped Bayern enjoy a record-breaking year which saw them become the first German team to win the treble of Champions League, Bundesliga and German Cup in the same season. Bayern also lifted the European Super Cup and FIFA Club World Cup in 2013.
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 presided over Bayern's unforgettable 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 boss, with former Manchester United boss Sir Alex Ferguson finishing in third spot.