Messi was involved in 63 goals in total in the past 12 months for both club and country, including 46 goals and 17 assists as the playmaker helped Barca to retain their La Liga crown.
"I would like to thank all of the journalists who voted for me and wanted me to have this prize," said Messi after picking up the award in Paris on Monday night alongside his two sons and wife.
"Thank you so much to my colleagues who have actually contributed a lot to this prize. It is amazing, thank you so much."
Messi was presented with the gong by 2018 winner Luka Modric and that means as well as this year, the Argentina international has also won the Ballon d'Or in 2009, 2010, 2011, 2012 and 2015.
The Barca captain beat Liverpool's Netherlands centre-back Virgil van Dijk into second place, while his long-time rival Cristiano Ronaldo was third in the voting, with Liverpool forward Sadio Mane fourth.
"It was an amazing year, but there's a couple of players like that who are a bit unnatural," said Van Dijk, of Messi and Ronaldo.
"So you need to respect greatness as well. I was close, but there was just someone a little bit better.
"I'm very proud of what I achieved last year with Liverpool and the Netherlands, and hopefully we can do that again this year. But that will be tough with those guys around here still."
Van Dijk admitted he had never expected to be in the running for the prestigious title.
"I never thought that I would be up for a Ballon d'Or until I was actually nominated," said Van Dijk.
"It shows a lot about how my career has been. My career has been different from the winner here, I came late, but I never gave up on my dreams.
"I had to work hard every step of the way, so to be here makes me very proud. And I want to work hard and be here again next year."
Meanwhile, Van Dijk's Liverpool team-mate Alisson won the inaugural Yashin Trophy for the best goalkeeper, ahead of Barca's Marc-Andre ter Stegen and Manchester City No 1 Ederson.
The other winner in the French capital was Juventus' summer signing Matthijs de Ligt, who took home the Kopa Trophy for the best U21 player of the past year.
The Netherlands international, 20, claimed the award ahead of Borussia Dortmund's England forward Jadon Sancho after helping his previous club Ajax to last season's Eredivisie title and the Champions League semi-finals.
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