Croatia reached the World Cup with a 2-0 win over Iceland on Tuesday. Simunic took up a microphone on the field after the match and shouted to fans: "For the homeland!" The fans responded: "Ready!"
The call was used by the Croatian pro-Nazi puppet regime that ruled the state during World War II.
The prosecutor office fined Simunic the equivalent of 3,200 euros ($4,300) on Thursday for "spreading racial hatred." It said he was aware this was the call used by the WWII regime.
Simunic has defended his action, saying he was driven by love for his country.
FIFA said it is considering disciplinary action against Simunic.