The 25-year-old enjoyed a fine year for club and country - winning a league and Champions League double before playing a pivotal role in Spain's World Cup success, where she also won the Golden Ball.
Bonmati beat Chelsea and Australia striker Sam Kerr into second place, with her Spain and Barcelona team-mate Salma Paralluelo coming third.
Two of England's Lionesses who reached the World Cup final made the top 10, with Manchester United goalkeeper Mary Earps fifth and Rachel Daly of Aston Villa 10th.
"I'm very proud to win the Ballon d'Or," Bonmati said.
"Football is a collective sport so I'd like to extend this prize to my team-mates and staff."
She added: "Finally congratulations to the other nominees. They're great footballers.
"As role models we have a responsibility on and off the pitch. We should be more than athletes and keep leading by example and fighting together for a better, peaceful and equal world."
Manchester City were crowned the men's team of the season after Pep Guardiola's side delivered the treble of Premier League, Champions League and FA Cup.
Meanwhile, City's Erling Haaland won the Gerd Muller Trophy for the world's top-scoring striker after hitting a record 56 goals last season.
Aston Villa and Argentina goalkeeper Emiliano Martinez won the Lev Yashin Trophy for goalkeeper of the year after his starring role in his nation's World Cup win.
England international Jude Bellingham was voted the Kopa Award winner for the best under-21 player in the world.
The Real Madrid and England midfielder picked up the trophy after the 20-year-old finished 18th for the main award.
Bellingham has hit 13 goals in 13 appearances since moving to Madrid in the summer, including a double to lead Real to victory in his first El Clasico against Barcelona on Saturday, but his success was for last season - where he shone for Borussia Dortmund and England.