Rapinoe was rewarded at the FIFA Best awards for leading the United States to the women's World Cup title in July, as was Jill Ellis who won the women's coach award.
Rapinoe scored six goals in the tournament, earning her the Golden Boot for the tournament's top scorer and the Golden Ball as the top player.
The outspoken star often uses her success as a platform to speak out about issues and the 34-year-old did so again in Milan, pleading for her male and female colleagues to join the likes of Manchester City winger Raheem Sterling in speaking out on racism and other inequalities.
"If we really want to have meaningful change what I think is most inspiring would be if everybody other than Raheem Sterling and (Kalidou) Koulibaly, if they were as outraged about racism as they were, if everybody was as outraged about homophobia as the LGBTQ players, if everybody was as outraged about the lack of equal pay and investment in the women's game other than just women, that would be the most inspiring thing to me," Rapinoe said.
"That's my ask of everybody. As professional footballers ... we have so much success, we have incredible platforms, I ask everybody here to lend your platform, to lift people up, to use this beautiful game to change the world for better."
Rapinoe finished with 46 ranking points to 42 for teammate Alex Morgan and 29 for England's Lucy Bronze.
After the ceremony, Rapinoe said being able to speak out about issues is more important to her than the actual award.
"I've been very lucky to have this incredibly platform that seems to be growing by the day and I plan to use it to the best of my ability," she told reporters. "The award's amazing of course but I don't do this for individual awards, certainly not.
"Even the team awards, the World Cup's obviously incredible to win but when we sort of all look back on it, it will be the way we've changed the game and moved the game forward and really been a part of changing the world, this incredible movement that's happening right now, that we'll all be most proud of."
Messi's award moved the Barcelona and Argentina forward one ahead of Cristiano Ronaldo. The Juventus forward did not attend the ceremony despite being among the three finalists.
The duo has dominated the award since 2008, with their string of victories only interrupted by Luka Modric last year.
Liverpool defender Virgil van Dijk was the other finalist
Messi finished with 46 ranking points to 38 for van Dijk and 36 for Ronaldo.
Aaron Long, given the U.S. captain's vote because he was among two players who wore the armband twice this year, voted for van Dijk, as did American coach Gregg Berhalter.
Van Dijk's club manager Jürgen Klopp was voted coach of the year after steering Liverpool to the Champions League title in June, while teammate Alisson won the best men's goalkeeper award.
"I have to thank my team because as coach you can only be as good as your team is," Klopp said.
Ellis also thanked her players.
"I owe so much to them," she said.
Ellis resigned in July, shortly after the U.S. beat the Netherlands 2-0 to win its second successive World Cup.
The 53-year-old Ellis was hired as coach of the U.S. team in 2014 and led it to eight overall tournament titles, including back-to-back World Cup successes. Over the course of her tenure, the United States lost just seven matches.
Her players made up nearly half of the women's team of the year, with Kelley O'Hara, Julie Ertz, Rose Lavelle and Morgan included in the 11 as well as Rapinoe.
"I think I walked out with Messi and no one noticed me," Ellis said jokingly to reporters, before adding: "It was such an honor, it really was. Fantastic night ... happy for my players to do so well as well on that stage so it was great."
The award for the best women's goalkeeper went to van Veenendaal of Atletico Madrid and the Netherlands.
The 29-year-old Van Veenendaal captained the Netherlands to the final of the women's World Cup.