The Real Madrid forward won the award, handed out by magazine France Football, for the second consecutive year having led his side to the La Liga title with 25 goals and a second consecutive Champions League crown, netting 12 goals including two in the 4-1 win over Juventus in the final.
Ronaldo also became the all-time leading scorer in Europe's top five leagues when he reached 366 goals in May to overtake Jimmy Greaves.
His two goals in Madrid's Champions League final victory over Juventus also took the Portugal star past 600 career goals, while Messi only reached the 500 mark for Barcelona six weeks earlier.
Messi came second while Paris Saint-Germain forward Neymar, the most expensive player in the world, was third. Veteran Italian goalkeeper Gianluigi Buffon finished fourth and Madrid midfielder Luka Modric came fifth.
Chelsea and France midfielder N'Golo Kante was the highest ranked Premier League player, coming eighth, while Tottenham Hotspur's Harry Kane, ranked 10th, was the only England player to make it into the top 10.
Ronaldo collected the trophy in a glitzy ceremony at the Eiffel Tower in the French capital, presented by former France player David Ginola.
"I feel very happy, it's a fantastic moment in my career," Ronaldo said upon collecting the award, standing with his mother Maria Dolores and his oldest son Cristiano Jr.
"I've waited a long time for this. This has been a stupendous year for me, we won the Champions League and La Liga and on a personal level I was top scorer in the Champions League.
"Trophies help me win prizes like this and I have to thank my teammates at Madrid and Portugal. They've been very important to me."
Ronaldo, who this year also helped the national side qualify for the World Cup in Russia next year, won his first Ballon d'Or in 2008 while with Manchester United and collected it again in 2013, 2014 and 2016.
The 32-year-old was last month named the Best FIFA Men's Player in the global football body's own awards ceremony.
The Ballon d'Or was first awarded in 1956 and was partnered with FIFA from 2010 to 2015, until last year becoming its own entity once again.
The Ballon d'Or is voted for by a jury of 173 journalists from around the world and presented by France Football, having ended their six-year partnership with FIFA, which ran from 2009 to 2015.
Ronaldo and Messi jointly hold the record for the most Ballons d'Or, having won five each and dominated the top two places in the standings since 2008.
The last player to beat either of them to the award was Kaka in 2007 and since then the pair have thrived on a rivalry that has defined a generation.