The Real Madrid forward was crowned player of the year on Monday at the FIFA Best ceremony at the London Palladium theatre attended by runner-up Messi and third-placed Neymar.
A second successive honor for Ronaldo was expected after a season in which the Portuguese eclipsed his award counterparts in the trophy stakes.
As well as Spanish league and Spanish Super Cup success, Ronaldo scored twice in the Champions League final against Juventus to win European soccer's elite competition for the third time in four seasons.
Ronaldo's coach at Madrid, Zinedine Zidane, was crowned coach of the year.
FIFA has shifted its award ceremony from its usual January slot to October so players are judged across a season - based on the typical European schedule - rather than the calendar year.
The women's award honored the Netherlands' success at the European Championship in August. Lieke Martens, who scored in the final win over Denmark, won the player's award and Sarina Wiegman collected the coaching accolade.
The Puskas Award for best goal went to Arsenal striker Olivier Giroud for a scorpion-style kick. The Puskas Award-winning goal from an overhead back-heeled strike came on New Year's Day in Arsenal's 2-0 victory over Crystal Palace in the English Premier League.