Rapinoe, Messi win FIFA player of the year awards
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.
His club manager Jürgen Klopp was named 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 US beat the Netherlands 2-0 to win its second successive World Cup.
The 53-year-old Ellis was named coach of the US 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 Alex 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.
AP
Most Popular
- CHINADA condemns media violating athletes' privacy
- CHINADA ready to cooperate with WADA in regular compliance review
- Chengdu hosts BWF Thomas and Uber Cup Finals 2024
- Soccer tournament for players with disabilities kicks off in Beijing
- China's Yuan, Dou looking to enjoy a hole lot of laughs
- Wild-card Shang smashes it in Madrid