The defender took to the microphone on the pitch after the 2-0 play-off win over Iceland at the Maksimir Stadium in Zagreb on Tuesday night and chanted "For the homeland!", to which fans responded "Ready!".
That was the cry used by the Croatian pro-Nazi puppet regime called the Ustashas, who ruled the state when thousands of people were killed in concentration camps during World War II.
Reports suggest Simunic could be disciplined by FIFA and the world governing body confirmed they are looking into the incident.
A FIFA spokesperson told Perform: "We are in the process of analysing the different match officials' reports and gathering information. We cannot comment further for the time being."
Australia-born Simunic, 35, was initially quoted as saying: "Some people have to learn some history. I'm not afraid."
However, the Dinamo Zagreb centre-back later released a statement through his club's official website denying any wrong-doing.
His statement said: "The thought that someone could put me in the context of hate speech is terrible to me.
"I don't want to be pathetic, but as a Croat raised outside his homeland, I associate 'home', love, warmth and positive struggle. Maksimir, Zagreb, Croatia - that's my home.
"If anyone understood me in a different, negative way, I hereby dismiss any political context of my words."
Goals from Mario Mandzukic - who was also sent off - and Dario Srna sealed Croatia's passage to Brazil after the first leg had finished goalless.
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