Luka Modric's performance at the 2018 FIFA World Cup helped him win the award as he captained his national team to the final of the championship where they lost to France.
Messi, meanwhile, claimed four Ballons d'Or as well as one FIFA World Player of the Year honour.
"The birth of the Ballon d'Or is a step further in the evolution of our sport, which is progressing well", France worldwide and Lyon star Wendie Renard told the magazine.
In addition, this year's Ballon d'Or will be awarded to a woman for the first time.
A version of the Ballon d'Or has been awarded by France Football magazine since 1956, but was merged with Fifa's World Footballer of the Year award from 2010 to 2015.
Modric's success means Ronaldo remains tied with Messi having won FIFA's award in different guises five times each.
The victor of the FIFA Award is picked after the votes are split between national coaches of FIFA Member Associations, their team captains, a select group of media from those countries, and fans. Each accounted for 25% of the total.
Messi was incredibly not nominated for the award, as Ronaldo, Luka Modrić and Mohamed Salah were deemed to have had better seasons than the Argentine.
Now with Real Madrid, the 26-year-old Courtois joked before his award was announced that Federation Internationale de Football Association should also hand out a save-of-the-year prize.
"It is possible that they won too much and do not like to lose".
Marta scored 13 goals and set up six more as Orlando Pride reached the NWSL play-off semi-finals in the United States - earning herself a place in the league's team of the year.
"I hope that Luka will be the best player in the world", Croatia manager Zlatko Dalic told AFP.
FIFA World XI: De Gea, Dani Alves, Raphael Varane, Sergio Ramos, Marcelo, Luka Modric, Kante, Eden Hazard, Lionel Messi, Kylian Mbappe, Cristiano Ronaldo. The coach award in the women's game went to Reynald Pedros, the Frenchman who led Lyon to French league and Champions League glory.