Leicester City's Claudio Ranieri received the best men's coach award following his side's fairytale Premier League triumph.
But the night again belonged to the 31-year-old Ronaldo, who edged out long-time nemesis Lionel Messi for the trophy as well as France's Antoine Griezmann, the top player at this summer's European championship.
Ronaldo had already won the Ballon d'Or after his third Champions League title, thanks largely to his 16 goals in 12 games, as well as triumphing with Portugal at Euro 2016 -- the country's first major prize.
"2016 was the best year of my career," Ronaldo said after being handed the prize from FIFA President Gianni Infantino.
Ranieri, 65, who saw off Real boss Zinedine Zidane and Portugal manager Fernando Santos, said the best coach honour was "incredible" after receiving the prize from Argentine football legend Diego Maradona.
Under Ranieri's leadership, Leicester pulled off one of the greatest shocks in English football history by defying title odds of 5,000-1 to lift the Premier League trophy last season.
Having miraculously avoided relegation the previous season, the Foxes rode that wave of momentum all the way to the title.
The prizes were based on a combined voting process involving national team coaches and captains, a select group of journalists and fans.
Ronaldo took 34.5 percent of the vote over 26.4 percent to Messi, who skipped the awards show co-hosted by US actress and former "Desperate Housewives" star Eva Longoria.
Barcelona said Messi was focused on preparing for an upcoming match against Athletic Bilbao.
- 'Bittersweet' -
US midfielder Carli Lloyd scooped the best women's player of 2016, the two-time Olympic gold medallist adding to her 2015 FIFA Women's World Player of the Year accolade.
The American finished ahead of Brazilian star Marta and Germany's Melanie Behringer.
She described 2016 as "bittersweet", with the US failing to win a medal for the first time in women's Olympic football.
Spain's La Liga accounted for nine of the 11 players in the FIFPro team of the year with Ronaldo and Messi headlining a star-studded line-up.
Ronaldo was joined by Real team-mates Sergio Ramos, Marcelo, Toni Kroos and Luka Modric while the side comprised four Barcelona players with Gerard Pique, Andres Iniesta and Luis Suarez joining Messi.
Bayern Munich goalkeeper Manuel Neuer -- named to the FIFPro World 11 for the fourth year running -- was the only player selected without links to Spain's top two clubs.
Juventus defender Dani Alves was included for a sixth time having helped Barca to a league and cup double before leaving the Camp Nou for Italy last June.
FIFA also gave a fair play prize to the Colombian side Atletico Nacional.
The team had asked South America's football governing body to award a regional club title to Chapecoense after most of the Brazilian side perished in a plane crash on the way to the first leg of the final.
- New honours -
World football's governing body launched the new award series after ending its six-year collaboration with France Football magazine for the Ballon d'Or.
The change is one of many implemented under Infantino, who took over FIFA last year pledging to lead it away from the scandals that dominated the end of Sepp Blatter's tenure.
Speaking on the so-called "green carpet" outside the Zurich awards venue, Maradona said the prizes helped define a new FIFA identity.
"After everything that was taken away from football, everything that was tainted by corruption, to see new people, new faces, that provides me with hope," Maradona said.
But the first 11 months of Infantino's administration have had their troubles, including massive and often contentious FIFA staff overhauls and an ethics probe that ultimately cleared Infantino of abusing his office.
Infantino's biggest test to date is set for Tuesday, when FIFA's powerful governing council will decide whether to back his controversial push to expand the World Cup to 48 teams from its current 32-nation format.