Manchester City and Spain star Rodri was awarded the 2024 Ballon d'Or at a ceremony in Paris on Monday evening following a day of drama surrounding the event.
Vinicius appeared to be the front-runner to claim the top prize after a leaked list suggested he was poised to beat Rodri.
However, it soon emerged that Rodri would claim the coveted trophy, leading Real Madrid to stop their delegation from attending the event.
Los Blancos subsequently released a statement to claim they would not attend an event where they are "not respected".
Ballon d'Or chief explains reason behind Vinicius defeat
The winner of the Ballon d'Or is decided by a vote by 100 journalists - one from each of FIFA's 100 top-ranked member nations.
Garcia, who is the editor-in-chief of the awards organisers France Football, has explained that the fact Dani Carvajal and Jude Bellingham finished in the top four ultimately split the vote for Vinicius.
"Obviously, Vinicius surely suffered from the presence of Bellingham and Carvajal in the top five because, mathematically, that took some points away from him," Garcia told L'Equipe television.
"This also sums up Real Madrid's season, which took between three and four players and the juries distributed their decisions among them, which benefited Rodri. What I can guarantee is that no one at Real Madrid or at Manchester City was aware.
Garcia expresses disappointment at Real Madrid's non-attendance
Garcia also admitted that he was "unpleasantly surprised" that Real Madrid decided against sending a delegation to the ceremony.
"Maybe they (Madrid) had a feeling, a strong feeling. Perhaps the Clasico (the 4-0 defeat by Barcelona) didn't help. I don't know. At the time that Real Madrid took its decision, I'm not sure that they knew 100 per cent that Vinicius hadn't won the Ballon d'Or.
"I was always clear, fair, and perhaps my silence took them to the limit. But it was the same as with the others. I was very unpleasantly surprised by its absence. We were very clear with them and with all the other clubs.
"This year, the winner was not going to be notified. I thought everyone had agreed but at the last moment, I don't know why, they wanted to change the rule."
While Vinicius missed out on the Ballon d'Or, Real Madrid picked up two awards despite their non-attendance at the event in Paris.
The European champions were named as the Club of the Year, while manager Carlo Ancelotti won the Men's Coach of the Year.