"It was an unbelievable year, but there's a couple of players like that who are a bit unnatural", said Van Dijk, of Messi and Ronaldo.
Ronaldo missed out past year too to Luka Modric.
That led to Rapinoe being named The Best FIFA Women's Player in September and she has now succeeded Ada Hegerberg by winning the second ever Ballon d'Or Feminin.
The 32-year-old put up impressive numbers on his way to the 2019 Ballon d'Or.
"If you have to give it to the best, let's just give it to Messi and the problem is solved", Barcelona boss Ernesto Valverde said ahead of the match.
Mo Salah is supposedly going to come in third ahead of five-time Ballon d'Or victor Cristiano Ronaldo. Not only that, but Van Dijk's Netherlands also came second to Portugal in the inaugural UEFA Nations League.
Arguably the greatest footballer to have played the game, Lionel Messi's had another brilliant year where he racked in plenty of goals and assists.
"I had to work hard every step of the way, so to be here makes me very proud". I am going to be there for a reason and there are no losers on the evening.
Megan Rapinoe capped her incredible year by winning the Ballon d'Or Féminin on Monday in Paris, presented annually now to the top player in women's soccer.
Two other Reds players polled in the top 10 after Champions League success, Egypt's Mohamed Salah (fifth) and goalkeeper Alisson Becker (seventh) of Brazil.
"So yes, he's incredibly important but if Virgil played the last line alone it would be pretty hard".
But having missed out in the Champions League, Messi's potential Ballon d'Or win would perhaps raise the debate that forwards get a stats-based boost over defenders when it comes to being considered for awards.
BeIn Sports broadcasted the awards ceremony in the United States past year and are expected to do so again in 2019.