Carlo Ancelotti and his Real Madrid players highlighted their frustration at the Ballon d'Or result on social media.
Vinicius Junior was a favourite to scoop football's biggest individual accolade on Monday.
However, reports emerged prior to the ceremony in Paris that the winger would not be winning the men's prize, with Manchester City midfielder Rodri taking it instead.
Madrid, who were named Team of the Year, did not send a single representative to the ceremony.
Ancelotti, meanwhile, won the inaugural Men's Johan Cruyff Trophy for leading Los Blancos to a LaLiga and Champions League double last season.
Jude Bellingham, Dani Carvajal and Kylian Mbappe all finished within the top six of the Ballon d'Or voting.
Ancelotti singled out Vinicius and Carvajal, who is now sidelined with a serious injury, for specific thanks.
"I want to thank my family, my president, my club, my players and above all Vini and Carvajal," the Italian wrote on social media.
In a statement to AFP and Spanish media, Madrid suggested if Vinicius had been overlooked, then it was not right for Carvajal, who scored in the Champions League final against Borussia Dortmund and also helped Spain win Euro 2024, should have won it instead.
"If the award criteria doesn't give it to Vinicius as the winner, then those same criteria should point to Carvajal as the winner," the Madrid statement read.
"As this was not the case, it is clear that [the] Ballon d'Or and UEFA do not respect Real Madrid. And Real Madrid does not go where it is not respected."
Vinicius' team-mate Eduardo Camavinga also used social media to outline his frustration at the result.
"FOOTBALL POLITICS X. My brother, you are the best player in the world and no award can say otherwise. Love you my bro," the France international posted on X.
Marta, an icon of the women's game, also shared her sympathy with her compatriot.
"I waited all year for Vini to be deservedly recognised as the best player in the world and now they come to tell me that the Ballon d'Or is not for him?" she said in a video on Instagram.
Vinicius subsequently posted on social media, writing on X: "I will do it 10 times if I have to. They're not ready."
Asked what Vinicius meant with his post, his management staff told Reuters that he was referring to his fight against racism and that they believe it was what led to him not winning the award.
They added: "The football world is not ready to accept a player who fights against the system."
The 24-year-old has been subjected to racial abuse on several occasions in Spain, leading to at least two convictions for racist insults in pioneer cases in the country.
France Football, which organises the Ballon d'Or awards, was not immediately available for comment.