Lionel Messi added to his 2009, 2010, 2011, 2012 and 2015 Ballon d'Or trophies; Rapinoe won Ballon d'Or Féminin after leading the United States to a record-extending fourth World Cup title in France this year
The Argentine, who won the Liga title with Barcelona but only managed third place in the Copa America with his country, added to his 2009, 2010, 2011, 2012 and 2015 trophies.
He finished above Dutchman Virgil van Dijk and Portugal's third-placed Ronaldo, who has won the award five times.
"I am very lucky, I am blessed. I hope I will continue for a long time," Messi told reporters. "I realize that I'm lucky even if one day it will be time to retire," added the 32-year-old.
"It will be tough but I still have some years ahead of me. Time flies so I will enjoy football and my family."
Van Dijk was one of four Liverpool players in the top 10, with Sadio Mane fourth, Mohamed Salah fifth and goalkeeper Alisson seventh. The latter won the Yashin trophy, a new prize for the goalkeeper of the year, named after former USSR icon Lev Yashin.
"It was amazing," said Van Dijk. "There are a couple of players like him (Messi) who are fantastic. I'm proud of what I've achieved with Liverpool and Holland. It's going to be tough (to win the award) when these guys are around."
Messi, whose stellar career was rewarded with another trophy, and Ronaldo, had between them won 10 consecutive Ballon d'Or awards until Croatia's Luka Modric prevailed in 2018.
It is the first time since 2010 that Ronaldo has failed to rank in the top two.
Megan Rapinoe earlier won the women's Ballon d'Or after leading the United States to a record-extending fourth World Cup title in France this year as they retained the trophy.
The 34-year-old midfielder, the standout player at the June-July tournament, succeeded Norway's Ada Hegerberg who did not take part in the World Cup.
Rapinoe was not present at the ceremony in the Theatre du Chatelet, where the show 'An American In Paris' is on.
"I'm so sad I can't make it tonight. It's absolutely incredible congrats to the other nominees. I can't believe I'm the one winning in this field, it's been an incredible year," Rapinoe said in a recorded message.
"I want to thank my team mates and the US federation."
Dutchman Matthijs de Ligt, a key player in Ajax Amsterdam's thrilling run to the Champions League semi-finals and now at Juventus, won the Kopa trophy for the best Under-21 male player.
There was, however, no trophy for the best female Under-21 player or keeper.