The Court of Arbitration for Sport (CAS), headquartered in Lausanne, said it had unanimously rejected an appeal by the Australian-born Simunic imposed by FIFA in December.
The ban starts with the World Cup where Croatia take part in the opening match against hosts Brazil on June 12th.
The world body FIFA hailed the ruling and Croatia accepted the verdict.
Simunic, 36, is one of Croatia's longest serving players with 105 caps.
But the Dinamo Zagreb defender caused outrage after Croatia's World Cup qualifying playoff against Iceland on November 19th, which Croatia won 2-0 to secure their berth in Brazil.
After the final whistle, Simunic went to the centre of the pitch in Zagreb with a microphone and yelled "u boj" and "za dom" — Croatian for "to the battle" and "for the homeland".
In response, fans chanted "spremni", meaning "ready".
The chant was the rallying cry of Croatia's World War II Ustase regime, a close ally of Nazi Germany.
The Ustase killed hundreds of thousands of Serbs, Jews, anti-fascist Croatians, Roma and others in concentration camps.
"The player stated that he did not have the intention to offend or discriminate anyone but that he wanted to share his patriotic emotions with the fans after such an important success," CAS said.
That argument failed to sway the CAS arbitrators.
"They confirmed that the expression used by Simunic was a clear and unequivocal reference to the call used by the Ustase and that such expression has to be sanctioned," it said.
Football's world governing body welcomed the ruling.
"With this decision, FIFA considers that CAS gives a clear and strong support to FIFA's efforts in stamping out racism in football," the Zurich-based organization said.
CAS is sport's final court of appeal.
Simunic asked it to either overturn the FIFA sanction or suspend it for a year, during which his behaviour would be on watch.
On top of the ten-match ban, the Dinamo Zagreb captain was also banned from even attending the games.
FIFA fined him fined 30,000 Swiss francs ($34,000).
Croatian prosecutors fined Simunic 25,000 kunas ($4,400) for inciting racial hatred, arguing that he was aware that the chant was an official Ustase salute.
Croatian Football Federation (HNS) chief Davor Suker said he felt "sorry for Josip."
"However, the positions of FIFA, UEFA and HNS on racism and discrimination are well known and such a decision is in line with that policy," Suker said in a statement.
He praised Simunic's contribution to Croatia's national squad.
"Josip gave an important contribution to our path to Brazil and the team will certainly play for him at the championship," Suker said.
Simunic was born to Croatian migrant parents in Canberra, Australia.
He has repeatedly maintained that his sole motivation was his love of Croatia and its people, and that any association with hatred or violence "terrifies" him.