Messi picked up 686 points to Van Dijk’s 679 as the Barcelona forward claimed his sixth Ballon d’Or by just seven points overall.
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A total of 176 journalists across the globe had their say, with five points awarded to their first pick, three for second and one for third.
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Messi's win sees him move one Ballon d'Or ahead of Cristiano Ronaldo, who was voted third ahead of Sadio Mane and Mohamed Salah.
French magazine France Football will reveal the full voting breakdown on December 4.
According to the Evening Standard, journalists from Europe and Asia deemed Van Dijk the world's best player, but Africa, Oceania and both North and South America favoured Messi.
Ronaldo reportedly picked up 476 points to Mane's 347 and Salah's 179.
Kylian Mbappe, Alisson Becker, Robert Lewandowski, Bernardo Silva and Riyah Mahrez completed the top 10.
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