The prayer was led by the deputy mufti for Croatia, Aziz Hasanovic. The head of the Islamic community in Croatia, mufti Sevko Omerbasic, was also in attendance.
Hasanovic said the 740 Muslims killed in the Homeland War sacrificed their lives in the creation of independent Croatia.
"Remembering the victims of the Homeland War, not just Muslims, but all, is our obligation," he said, adding that in democratic Croatia Muslims could practice their religion.
On Omerbasic's decision, those killed in the Homeland War were remembered in all Islamic religious centres in Croatia today.
"There are many divisions in today's world, not just religious and national. Everything is relativised, especially morality," Omerbasic said, calling on the Muslim faithful to preserve genuine faith.