The Argentina international, who has become the second player in history to win the prestigious award three times in a row, was chosen ahead of Barca team-mate Xavi and Real Madrid forward Cristiano Ronaldo.
Messi dedicated the award to his Barca and Argentina team-mates, but made a special mention to Xavi, who has yet to win the Ballon d'Or accolade despite being nominated in the last three years.
"It is a huge pleasure and honour to win my third award [of this kind]," Messi said. "I wanted to share it with those who voted for me, my coach and my team-mates at Barca and in the Argentina national team.
"Moreover, I want to share this award specially with my friend Xavi. This is the fourth time that we are together at this ceremony and it is a pleasure for me to be with him on the pitch.
"I hope we can win more things together."
Messi amassed 47.88 per cent of the votes, ahead of Cristiano Ronaldo (21.6%) and Xavi (9.23%).
Starting in November and continuing through January, Goal.com is publishing exclusive extracts from Graham Hunter's highly-anticipated new book, 'Barca: The Making of the Greatest Team in the World'. Last Friday's extract took a closer look at the most influential figure in the club's history: Johan Cruyff: Don't miss it!