Messi claimed the award for the third time, but the eight-time Ballon d'Or winner was a surprise victor ahead of Erling Haaland on an otherwise glorious night for Manchester City.
The award only covered the period after Messi had led Argentina to World Cup glory in December 2022 to August 2023.
Messi had a subdued end to his career at Paris Saint-Germain, despite winning the League 1 title, before joining MLS side Inter Miami in June.
Messi quickly made his mark in the United States as he helped the franchise, part-owned by David Beckham, to their first trophy by winning the Leagues Cup in August.
Haaland was favourite to win after scoring 52 times in his debut season with City as the English side won a treble of Champions League, Premier League and FA Cup.
However, after receiving the same number of points from a scoring system based on votes from national team captains, coaches, journalists and fans, Messi was crowned victor thanks to more first-choice nominations.
Messi's former club teammate Kylian Mbappe was third.
Bonmati's selection as the best women's player was less controversial as she completed a clean sweep of personal awards after helping Spain to win the World Cup and Barcelona to Champions League glory in 2023.
She also won the Ballon d'Or, Golden Ball for Player of the World Cup and UEFA's Player of the Year in recent months.
"A couple of weeks ago when 2023 came to an end I was nostalgic because 2023 was an exceptional and unique year I will remember for the rest of my life," said Bonmati.
"I'm proud of being part of a powerful generation of women who are changing the rules of the game and the world."
Pep Guardiola was named best coach after masterminding City's first-ever Champions League success.
Haaland was joined by five of his club teammates - Kyle Walker, John Stones, Ruben Dias, Bernardo Silva and Kevin De Bruyne - in the team of the year.
Real Madrid's Thibaut Courtois, Jude Bellingham and Vinicius Junior, Messi and Mbappe made up the 11.
City's Ederson won men's goalkeeper of the year, while England and Manchester United stopper Mary Earps picked up the women's award.
England national team boss Sarina Wiegman won the women's coach of the year after leading the Lionesses to the World Cup final.
The Brazilian men's team won the Fair Play award after they dawned an all-black shirt for the first time in a show of support for forward Vinicius, who suffered several incidents of racist abuse while playing for Real Madrid last year.
There was also Brazilian success in the Puskas award for the best goal, scored by Botafogo's Guilherme Madruga for his spectacular overhead kick.
