Good form Messi is now on to 10 goals for the season in Blaugrana colours, and that's despite starting the campaign with a calf injury.
England's Lucy Bronze and the US's Alex Morgan completed the podium.
"I'm so sad I can't make it tonight", Rapinoe said on video. It's absolutely incredible congrats to the other nominees.
Rapinoe was one of four members of the United States side that lifted the World Cup to be nominated for the prize, along with Tobin Heath, Rose Lavelle and Alex Morgan, who finished third on Monday.
"I want to thank my teammates and the USA federation".
Liverpool can feel a bit look down because they couldn't get this trophy.
France Football magazine has been awarding the Ballon d'Or since 1956 and created a women's award for the first time previous year when Norway's Ada Hegerberg won it. Hegerberg was fourth this time.
Messi scooped the prize ahead of Virgil van Dijk, Cristiano Ronaldo and Sadio Mane.
The suspense surrounds the identity of the men's victor, 12 months after Croatia's Luka Modric claimed the crown thanks to his exploits in dragging his country to the World Cup final and winning the Champions League with Real Madrid. "There are a couple of players like him (Messi) who are fantastic. I am very proud", Van Dijk said. "It's going to be tough (to win the award) when these guys are around".
Cristiano Ronaldo brought the trophy home in 2016 and 2017, whereas Luka Modric was the victor a year ago. It's that time of the year when we witness the crowning of the world's best men's footballer.
Van Dijk, the victor of UEFA's Men's Player of the Year, could have been the first defender to lift the Ballon d'Or since Italy's Fabio Cannavaro in 2006, but he was left to settle for second place as Messi added another honour to the Best FIFA Men's award he received in September.
Alisson is the first victor of the new Yashin Trophy for the best goalkeeper, named after former USSR icon Lev Yashin.