The award was handed to the Barcelona and Argentina captain at a ceremony in Milan.
Messi, 32, led Barcelona to a fourth La Liga title in the past five seasons, scoring 36 goals and providing 15 assists in 35 league matches last campaign. He posted 51 goals and 22 assists in all competitions.
Croatia and Real Madrid midfielder Luka Modric won the award last year -- as well as the Ballon d'Or, which is awarded by France Football -- breaking up a decade-long duel between Messi and Ronaldo for the prize.
However, this is Messi's first The Best award, having gone without a top personal honour since 2015.
Ronaldo and Messi had won every main individual honour since Kaka's triumph in 2007. They each won the last two FIFA World Player of the Year awards -- Ronaldo in 2008 and Messi in 2009 -- as well as the Ballons d'Or in those years.
From 2010, the two awards merged and became the FIFA Ballon d'Or with Messi claiming four in a row. In 2013 and 2014, the Ballon d'Or returned to Ronaldo before Messi won a fifth in 2015.
In 2016, FIFA introduced The Best award, which ran alongside the Ballon d'Or and Ronaldo won both that year and retained them in 2017 before Modric's clean sweep in 2018.
Messi's win is somewhat of a surprise with Van Dijk, a centre-back who transformed Liverpool's defence on the way to the Champions League crown, having won the European best player award.
In the final voting, Messi finished with 46 points, while Van Dijk (38 points) and Ronaldo (36) finished second and third respectively. The rest of the top 10 was rounded out by Liverpool forwards Mohamed Salah (26) and Sadio Mane (23), Paris Saint-Germain striker Kylian Mbappe (17), former Ajax midfielder Frenkie de Jong (16), ex-Chelsea forward Eden Hazard (16), ex-Ajax defender Matthijs de Ligt (9), and Tottenham striker Harry Kane (5).
Additionally, Debrecen forward Daniel Zsori won the Puskas Award for his overhead kick against Ferencvaros during a Hungarian league match.
Liverpool boss Jurgen Klopp took home coach of the year, while Reds goalkeeper Alisson was named best keeper.
United States head coach Jill Ellis and midfielder Megan Rapinoe collected women's coach and player of the year, respectively, for the USWNT's World Cup triumph this summer, while Netherlands goalkeeper Sari van Veenendaal was voted women's goalkeeper of the year after helping her country to the final of the competition.
Leeds manager Marcelo Bielsa was given the fair play award.