Rapinoe was not present at the ceremony to collect soccer's most prestigious individual accolade in the Theatre du Chatelet, where the show 'An American In Paris' is on.
"I'm so sad I can't make it tonight. It's absolutely incredible congrats to the other nominees. I can't believe I'm the one winning in this field, it's been an incredible year," Rapinoe said in a recorded message.
"I want to thank my team mates and the U.S. federation."
Dutchman Matthijs de Ligt, a key player in Ajax Amsterdam's thrilling run to the Champions League semi-finals and now at Juventus, won the Kopa trophy for the best Under-21 male player in the world following a vote of international journalists.
Alisson Becker, one of four Liverpool players in the top seven for the men's Ballon d'Or, was awarded the new Yashin trophy for the best male goalkeeper of the year.
There was, however, no trophy for the best female Under-21 player or goalkeeper.
The men's Ballon d'Or will be presented later on Monday. (Reporting by Julien Pretot; Editing by Ken Ferris)