Croatia booked their spot at next year's showpiece in Brazil with a 2-0 win over Iceland on Tuesday, but Simunic's celebrations have attracted criticism.
After the match, Simunic took a microphone on to the field and shouted to the fans in Zagreb: "For the homeland". The fans responded to Simunic's cry by shouting: "Ready!"
The call was used by the Croatian pro-Nazi puppet regime, the Ustashas, who ruled the state when thousands of people were killed in concentration camps during World War II.
Simunic has been fined €3,200 by the prosecution office, who said he was "spreading racial hatred".
The Australian-born defender, who is 35 years old, was initially quoted as saying: "Some people have to learn some history. I'm not afraid."
The Dinamo Zagreb centre-back later released a statement on his club's official website, dismissing any political context to his comments.
Simunic could yet face further disciplinary action, with FIFA revealing to Perform on Wednesday that they were still investigating the matter.
