The Portugal captain clinched the award for the second time in his career over the Argentine and Franck Ribery and the Barcelona star insists he has "no complaints".
Ronaldo clinched the award for the second time in his career after a stellar 12 months for club and country in which he scored 69 goals in just 59 appearances, beating Messi and Bayern Munich's Franck Ribery who finished second and third respectively.
Messi, who had won the previous four Ballons d'Or, admits he is disappointed to have missed out on a fifth-consecutive prize but maintains the injury problems which affected his chances this year should not detract from Ronaldo's achievement.
"He had a great year, so there is nothing else to say. It was a good year for the three of us and that's why the three of us were there. Whoever won it would have been a worthy winner," Messi told reporters in Zurich. I don't know if it would have been different if I hadn't been injured, but I was out for a long time. It meant I wasn't in the best shape at the end of the Champions League and meant I started the season injured. I was a long time out, but that has nothing to do with it. Cristiano had a great year and he won it on merit.
"Let's hope I will be back next year and the club is represented again, just like this year with the four players in the FIFPro XI. I wanted to win it, of course, I always like to win, but as I say I have no complaints; Cristiano is a worthy winner, he deserves it."
When asked if winning the previous four made missing out on the 2013 prize more of a blow, Messi added: "No, I wanted to win it – that doesn't make any difference."