Guinea's Under-23 men's team beat their Indonesian counterparts at France's Clairefontaine on Thursday after a penalty scored by Ilaix Moriba, who plays for Getafe in Spain on loan from Germany’s Red Bull Leipzig.
If Indonesia had won, they would have played football at an Olympics for the first time in nearly seven decades, since the Soviet Union eliminated them from the 1956 Games in Melbourne.
But after Guinea secured the final Olympic spot, some Indonesian fans bombarded the African nation's social media accounts as well as those of its top players.
"The players go home with their heads held high and accepted defeat. So, we hope the supporters will do the same," said football association executive committee member Arya Mahendra Sinulingga in a statement.
He said the Red and Whites regretted the racist comments online by Indonesian fans and said those behind them were not true supporters.
"Don't tarnish the Indonesia U-23 national team's struggle with racist remarks towards opposing players," he said.
"The dreams of these young people are still long. Please don't let it be harmed by racist actions which are very detrimental and embarrassing. We are focused on supporting the national team going forward."
Guinea will now play in Group A alongside host nation France, USA and New Zealand.
It will be their first appearance in the Olympic football tournament for 56 years, according to global football body FIFA.
