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 beat Virgil van Dijk, the runner-up, and third-placed Cristiano Ronaldo of Portugal, who has won the award five times.
“Ten years ago I received my first Ballon d’Or, guided by my three brothers,” Messi told the audience. “Today I receive my sixth, guided by my wife and children.”
Senegal’s Sadio Mane, who with Van Dijk and fellow nominees Alisson Becker of Brazil and Egypt’s Mohamed Salah, helped Liverpool win the Champions League, was fourth in the poll of international journalists.
“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 sterling career was once again rewarded, and Ronaldo, between them had won 10 consecutive Ballon d’Or awards until Croatia’s Luka Modric prevailed in 2018.
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 U.S. 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.
Alisson, one of the four Liverpool players in the top seven for the men’s Ballon d’Or, was awarded the new Yashin trophy for the best male goalkeeper of the year.
There was, however, no trophy for the best female Under-21 player or keeper.