The 32-year-old Argentine forward won the prestigious award for the first time back in 2009.
Megan Rapinoe had already been recognised earlier in the evening with the women's award, England's Lucy Bronze in second and another American World Cup-winner Alex Morgan in third.
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Ronaldo finished behind Van Dijk, who won the Champions League with Liverpool and earned second place in the voting, but was not present to see Messi posing with yet another golden trophy.
"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."
The three-man shortlist for the men's award was announced in advance but the organisers - magazine France Football - also counted down their top 30 players of 2019 in anticipation of the award.
Four Liverpool players, Van Dijk joined by Sadio Mane, Mo Salah and Yachine Trophy winner Alisson Becker, made it into the top 10 while reigning Premier League champions Manchester City had two representatives in Bernardo Silva and Sergio Aguero.
Van Dijk said: "It was amazing.
"There are a couple of players like [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."
Rapinoe earned her award 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 summer 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.
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.
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