Fifa has begun disciplinary proceedings against Josip Simunic and Croatia for the events that followed the World Cup play-off win over Iceland.
Defender Simunic, 35, was fined £2,600 by Croatian prosecutors for "spreading racial hatred" after appearing to lead fans in a chant with pro-Nazi connotations following
the 2-0 win.
He denies any political intent.
But Croatian prosecutors say he knew the chant was used by the country's pro-Nazi regime during World War II.
Fifa was awaiting a report from match officials and gathering information from Football Against Racism in Europe observers before deciding whether to take action.
“Even the thought that someone could put me in the context of incitement of hatred or violence is horrible”
A spokesman has now told BBC Sport: "Proceedings were opened against Simunic for his own behaviour and other proceedings were opened against Croatia for improper conduct of the spectators."
Footage shows Simunic shouting "for the homeland" over a microphone - the fans respond "ready".
The chant has associations with the Ustasha, Croatia's rulers during World War II.
The Dinamo Zagreb player was celebrating with team-mates and supporters after the southern Europe side reached next summer's finals in Brazil with
Tuesday's 2-0 victory in Zagreb.
Australia-born Simunic said in a statement released on Wednesday: "Even the thought that someone could put me in the context of incitement of hatred or violence is horrible.
"As a Croatian who was born and grew up outside my homeland, I associate home with love, warmth and positive struggle - everything that we showed on the pitch to win our place in the World Cup.
"And these were the only reasons I got carried away with my emotions and why I started the kind of exchange with the supporters."
The chant, coupled with the Nazi salute, has been used by Croatia fans in the past, leading to disciplinary punishments from Fifa and Uefa.
Immediately after Tuesday's match, Simunic said: "Some people have to learn some history. I'm not afraid. I'm supporting my Croatia, my homeland. If someone has something against it, that's their problem."