Messi, 32, received the award in 2009, 2010, 2011, 2012 and 2015, adding one more Ballon d'Or for the Best FIFA Men's award in 2019.
The excited reaction of Messi's son Mateo quickly went viral online after the Argentinian was announced as the victor.
Senegal's Liverpool striker Sadio Mane was fourth in the poll of global journalists.
Liverpool pair Sadio Mane and Alisson Becker are fifth and sixth respectively in this list, ahead of Kylian Mbappe in seventh.
Rapinoe, who plays club football for Reign FC in the USA, added: "I'm so sorry I can't be there".
"I'm proud of what I've achieved with Liverpool and Holland. But that will be tough with those guys around here still".
The Reds have opened up a big lead at the top but Saturday's 2-1 victory over Brighton was a nervy affair and the team have now gone 12 games without keeping a clean sheet in all competitions. He scored fifty-one times in forty-nine appearances last season while also providing twenty-two assists as Barcelona won the domestic title.
An apparently leaked document placed Messi first in the vote for the best player in the world, ahead of Van Dijk second and his Liverpool team-mate Mohamed Salah in third.
In other awards, Dutchman Matthijs de Ligt, a key player in Ajax Amsterdam's thrilling run to the Champions League semifinals and now at Juventus, won the Kopa trophy for the best Under-21 male player in the world following a vote of global journalists.
Winger Rapinoe, 34, co-captained the USA to victory at this summer's World Cup, where she was named player of the tournament and finished joint-top scorer with six goals. It's absolutely incredible congrats to the other nominees.
Matildas star Kerr's five goals at this year's Women's World Cup left her behind only England's White and Americans Rapinoe and Morgan.
Liverpool won the UEFA Champions League title in June thanks in large part to the contributions of Virgil van Dijk, who is still in the running to become the first defender to lift the Ballon d'Or since 2006.
"So yes, he's incredibly important but if Virgil played the last line alone it would be pretty hard".