Bonmati retained the Fifa women's player of the year award ahead of Zambia's Barbra Banda and Norway's Caroline Graham Hansen, having also won the women's Ballon d'Or for the second consecutive year in October.
The 26-year-old helped her club to a domestic treble last season in a campaign in which Barca also retained the Champions League, and Bonmati scored in the semi-final and final when Spain won the Nations League in February.
"I'm very grateful for this award, but I always say that this is a team effort, with a Barca that won everything and the national team," Bonmati said.
Real Madrid's Carlo Ancelotti won the best men's coach award, after the Italian led his club to the league and Champions League double last season.
"I want to share this with the club, with my president and with my players, those of the best club in the world," Ancelotti said.