Croatian President Ivo Josipovic, Prime Minister Zoran Milanovic and their wives attended the liturgy, with Metropolitan Jovan saying the arrival of the state leadership brought joy, honour and encouragement.
"Pacifism elevates man to the highest level of dignity, progress and blessing in society," the metropolitan said, calling on the faithful to let themselves be guided by God's mercy and a clean conscience.
He wished the Orthodox faithful a merry Christmas and a blessed New Year.
The service was also attended by Serb People's Council president Milorad Pupovac and Serbian Ambassador Stanimir Vukcevic.
In an interview with Nova TV, Metropolitan Jovan said, in the context of the economic crisis in Croatia, that society's problems lay also in a big moral crisis, especially in light of the "general problem of corruption" and a pronounced egoism. He said a psychological change was necessary to make people feel love for work and creativity.
Commenting on the polemic on sex education in schools between Education Minister Zeljko Jovanovic and representatives of the Catholic Church and some non-governmental organisations, Metropolitan Jovan said there was "a certain tendency which is in conflict with the Christian morality."
He said the Archbishop of Zagreb, Cardinal Josip Bozanic, spoke about the issue in a dignified manner and that the Church was interested in solving it in the best way.
If 80 per cent of Croatia's population is religious, "this has to be respected and taken into account" and "a minority cannot impose some of its positions, although it has to be clear what is true and what isn't, what is good and what isn't," said the metropolitan.
He was asked about an initiative by the Croatian Helsinki Committee on Human Rights on the establishment of a commission to investigate the crimes committed at the Jasenovac concentration camp in WW2.
Metropolitan Jovan said he had been engaged in the renovation and blessing of a church in Jasenovac and that what happened there had been a big tragedy, regardless of ethnicity or religion.
Asked about crimes committed in times of Communism, "crimes committed in peace", he said that had also been a big tragedy.
I remember from my childhood that many people disappeared overnight. There were no regular court proceedings. If a man is proven guilty, he should be held to account for his actions. But it was a matter of politics, ideology and a negative stance towards those who thought differently, so that all those conflicts were a big tragedy that happened in this region, Metropolitan Jovan said.
He said he was very glad to have met Croatian Army General Ante Gotovina, who was acquitted by the Hague war crimes tribunal last year, at President Josipovic's Christmas reception.
As laymen and observers, we can comment as we choose on what the tribunal has in its records and its competence, but a soldier must carry out his commander's orders. The general is in the same position as the soldier, he said.
Regarding the future of the people in Croatia and the region, Metropolitan Jovan said one should first and foremost help refugees return to their states because they were in a difficult situation, regardless of ethnicity or religion.