Mane came fourth in the final standings with 347 votes from the panel of world football journalists, behind winner Lionel Messi (686 votes) of Barcelona, Liverpool team-mate Virgil van Dijk (679) and Juventus forward Cristiano Ronaldo (476).
As well as helping his team to Champions League glory in June, Mane has continually excelled in domestic action for the Premier League's runaway leaders and Kouyate, who was part of the Palace team that lost 2-1 to Mane's Liverpool in November, suggested the 27-year-old was overlooked due to an anti-African bias.
"For me this Ballon d'Or is for Sadio Mane, there is no doubt about that," Kouyate told the Mirror.
"Listen, if Sadio was a Brazilian or a European there would not have been no debate.
"It would have been him for the award straight away and it's not because I play with him at international level, or because I know him; it's just what people who watch football feel.
"Just go back and watch what he did for both club and country and you will see in between the lines that no one has been better than him."
Kouyate added: "We all know that Messi is really good, maybe the greatest player, but last season, come on.
"Maybe it's not just football that they look at because there is no way three people had a better season than him [Mane].
"It's just unbelievable how some people are judged but that is not fair."
Liberia's George Weah is the only African recipient of the Ballon d'Or, winning it in 1995 ahead of Jurgen Kliinsmann and Jari Litmanen.
Mane's Liverpool team-mate Mohamed Salah finished in fifth in the 2019 Ballon d'Or standings, with Kylian Mbappe (sixth), Alisson (seventh), Robert Lewandowski (eighth), Bernardo Silva (ninth) and Riyad Mahrez (10th).