Soldiers of the Nazi-style Ustasha regime, killed during a battle in January 1943 in the town of Krasic, were thrown into the pit by the Partizans. The pit also contains the bodies of wounded people and medical staff, including nuns, who were taken from hospitals and thrown into the pit in May and June 1945, in the wake of the WWII.
The commemoration at Jazovka has been organised on 22 June every year since the discovery of the pit 20 years ago, as this is the day when Croatia also marks Anti-Fascist Struggle Day as a national holiday.
This year's commemorative event brought together about 3,000 people, including families of the pit victims, said the event's organiser, the Croatian Ceremonial Unit Jazovka.
During mass, Sarajevo Archbishop Cardinal Vinko Puljic said that people should not be afraid of the past but accept it and bequeath it to future generations.
Crime cannot be justified by crime, and hatred cannot be overcome by hatred, the Catholic dignitary said.
The memorial service was performed by a score of Catholic and Greek Catholic priests.
Prayers were also said by Idriz Efendi Besic, the envoy of the Grand Mufti of Croatia, Sevko Omerbasic.
A proclamation made by the above mentioned Jazovka Unit was read out to those who gathered near the pit.
The proclamation calls for establishing the historical truth about Croats, victims in WWII as well as in the wake of that war and during what it described was the totalitarian Yugoslav Communist system.
The proclamation urges the implementation of documents of the United Nations, the Parliamentary Assembly of the Council of Europe, the European Parliament, the Croatian Parliament and international treaties and conventions on bringing to justice criminal perpetrators and on indemnification for victims.
The proclamation insists on the removal of "the remaining disguised protagonists of the Yugoslav Communist totalitarianism from the authorities and public administration".
It calls for the condemnation of the "Yugoslav Communist criminal system and mindset."
The paper also accuses "the alleged antifascists" of celebrating their "false and empty holiday of anti-Croat Yugoslav Communist insurgence", adding that celebration in Brezovica Forest of "the Communist-Chetnik Insurgence of 22 June 1941" means the repetition of the "murder of martyrs" at all sites where crimes such as the atrocities in Jazovka have taken place.
The proclamation also reads that the present-day Croatia was established during the Homeland Defence War in the early 1990s and that it was not Tito's Partizans who founded Croatia.
In the eastern city of Djakovo, another commemoration in tribute to victims killed by Tito's Partizans in the wake of WWII was held earlier on Tuesday.
The commemorative event was held at a monument erected last year to some 80 residents of Djakovo who were killed by the Partizans when they entered that eastern Croatian town in April and May 1945.
There are 29 mass graves in the area of Djakovo dating back from the period immediately after WWII.