The decision to award the prize for the world's best player to the midfielder came as a surprise, with Real Madrid's Liga and Champions League double winner Vinicius Junior widely seen as the favourite.
Hours before the ceremony in Paris, the Spanish club announced its delegation would not attend the ceremony at Chatelet Theatre because of what it perceived as a snub of Vinicius.
Rodri, 28, played a key role as City held off Arsenal to win the Premier League title last season and was named player of the tournament at Euro 2024 as unfancied Spain emerged triumphant in Germany.
Rodri was diplomatic when addressing the question of Real's no-show in his post-award press conference.
"They have their decision, they didn't want to be here for their reasons," he said. "I just focus on my club and my team-mates."
Despite the French organisers insisting that the identity of the winner was a closely guarded secret this year, the news appeared to have leaked ahead of the festivities.
Barcelona and Spain star Aitana Bonmati earlier won her second successive women's Ballon d'Or, after leading her club to a historic continental quadruple of titles and claiming the Nations League with her country.
The drama started hours before the ceremony as Spanish and European champions Real said if Vinicius was not the winner, then the award should go to his teammate Dani Carvajal.
Like the Brazilian, Carvajal scored in the 2-0 victory against Borussia Dortmund in the Champions League final at Wembley.
Vinicius scored 24 goals and made 11 assists in 39 matches across all competitions for Madrid as he led the club to three titles last season.
"If the award criteria doesn't give it to Vinicius as the winner, then those same criteria should point to Carvajal
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