It capped a successful 2016 for Ronaldo, who captained Portugal to its first major international honor
at the European Championships in France.
He also scored the winning penalty as Real Madrid defeated city rival Atletico Madrid to win the UEFA Champions League for the second time in three seasons
Ronaldo has now won just one less Ballon d'Or than 2015 winner Messi, whose Barcelona team beat Real Madrid to the Spanish La Liga title by one point.
Messi missed out on his first international title when Argentina lost to Chile in June's Copa America final
-- he said that would be his last game for his country, but reversed that decision in August.
Ronaldo was unable to attend the awards ceremony in Paris as Real Madrid had traveled to Japan to take part in the FIFA Club World Cup, holding a six-point lead over Barca in La Liga after Saturday's win over Deportivo La Coruna.
"For me it's an unbelievable moment, I'm so proud, so happy," he said in a pre-recorded interview
. "Thank you to everyone who voted for me. Thank you to my teammates ... Portugal national team, and this trophy's for Real Madrid."
Although the 31-year-old had to leave the field after just 25 minutes of the Euro 2016 final against host nation France due to injury, his three goals and three assists had helped drag Portugal to the latter stages of the tournament.
It only qualified for the knockout rounds as one of the best third-placed group teams, drawing with Iceland, Austria and Hungary.
Following the end of its merged agreement with football's governing body FIFA, the 2016 Ballon d'Or award -- now run solely by its founder France Football magazine -- was decided by a vote of 173 journalists for the 30 nominated players.
In 2010-15, it also featured votes from national team captains and managers.
FIFA will award its own prize for the world's top performing player
-- with Ronaldo, Messi and Atletico Madrid striker Antoine Griezmann
shortlisted -- in a ceremony due to be held on January 9 in Zurich, Switzerland.
Griezmann, who was top scorer at Euro 2016 with six goals for losing finalist France, was third behind Messi in the Ballon d'Or voting.
Messi's Barca clubmates Luis Suarez and Neymar were fourth and fifth respectively ahead of Real's Gareth Bale, a semifinalist at Euro 2016 with Wales.
Ronaldo's success was foreshadowed late Sunday when an image purporting to show a leaked front cover of the latest edition of France Football -- declaring him the winner -- appeared on social media late Sunday.
Ronaldo first won the coveted prize in 2008, doing so again in 2013 and 2014. He and Messi have been the only winners since Brazil's Kaka took the honor in 2007.