Rapinoe was not at the Chatelet Theatre in the French capital, unable to make the trip back to the country where she led the USA to victory in July.
However, Messi was there with his wife, Antonella Roccuzzo, and two of their children. Now aged 32, it is Messi's first Ballon d'Or since 2015 and his sixth overall as he moves one ahead of old rival Cristiano Ronaldo.
"It is 10 years since I won my first Ballon d'Or here in Paris and I remember coming here with my three brothers, I was 22 and it was all unthinkable for me what I was going through," Messi said on stage after receiving the award from last year's winner Luka Modric.
"Now 10 years on this is my sixth, in a very different time, very special in my personal life with my wife and three children."
Van Dijk comes second
The Barcelona number 10 took the prize -- organised by France Football magazine and voted for by a panel of journalists from around the world -- from Liverpool defender Virgil van Dijk, with Ronaldo third.
It is the first time since 2010 that Ronaldo -- who last won the Ballon d'Or in 2017 -- has failed to rank in the top two.
Having starred in the Liverpool team that won the Champions League, Van Dijk finished second to Messi just as he did in the voting for FIFA's equivalent prize, The Best, in September.
"Unfortunately there are a couple of players like him who are a bit unnatural. Six times Ballon d'Or -- you need to respect greatness as well," said Van Dijk.
Van Dijk was one of four Liverpool players in the top 10, with Sadio Mane fourth, Mohamed Salah fifth and goalkeeper Alisson seventh. The latter won a new prize for the goalkeeper of the year, named after former USSR icon Lev Yashin.
Messi has scored 46 goals in 54 matches so far in 2019, and netted 36 times in total in 34 La Liga matches last season as Barcelona won the title.
He did not enjoy a successful Copa America with Argentina but was also the top scorer in last season's Champions League with 12 goals.
As if any reminder of his brilliance were required, on Sunday he scored a wonderful late winner for Barcelona against Atletico Madrid.
'Incredible year' for Rapinoe
This is just the second year that a women's Ballon d'Or -- voted for by a smaller panel of 48 journalists -- has been awarded, with Rapinoe succeeding Norway's Ada Hegerberg as the winner.
The prolific Hegerberg starred as Lyon again won the Champions League, but her self-imposed exile from her national team prevented her from featuring at the World Cup.
Rapinoe, meanwhile, was the star of that tournament on and off the field.
She won the Golden Boot for top scorer, with six goals, and Golden Ball for best player. Rapinoe scored the opening goal from the penalty spot as the USA beat the Netherlands 2-0 in the final.
But the 34-year-old feminist icon made headlines with her outspoken criticism of US President Donald Trump during the tournament and by leading the calls for her team to be paid the same as their male counterparts.
"It's been an incredible year," said Rapinoe in a recorded video message.
"I want to say a huge thank you to my team-mates, the coaches, the US Soccer Federation, for all of the support to allow me to be who I am and do what I do on the field but also be the person who I am off the field."
Rapinoe was one of four members of the US 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.
England's Lucy Bronze, who won the Champions League with Lyon before reaching the World Cup semi-finals with her country, losing to the US, came in second in the Ballon d'Or.
Matthijs de Ligt succeeded Kylian Mbappe as the winner of the Kopa Trophy for the best player aged under 21.
The defender starred in the Ajax side who reached the Champions League semi-finals and won the Dutch title, before joining Juventus in the close season.