Schools, courts and government offices were closed as Christodoulos was accorded honours typically granted to heads of state, reflecting the power of a church that represents 97 per cent of Greece's native-born population.
Earlier, Ecumenical Patriarch Bartholomew I, the Istanbul-based spiritual leader of the world's 250 million Orthodox Christians, led the morning prayers at Athens cathedral on Thursday.
The service was attended by Costas Karamanlis, Greece's prime minister, Karolos Papoulias, the country's president and top Orthodox officials.
Bartholomew said: "The archbishop's death was a great loss for the Orthodox world."
Christodoulos, who was 69, died of cancer at his Athens home on Monday, prompting an outpouring of public grief.
Preceded by long files of robed priests, the archbishop's casket was borne for 1.5km to Athens' First Cemetery, near the 1,800-year-old temple of Zeus, accompanied by a 900-soldier guard of honour.
Flags hung at half-staff across Athens and on the ancient Acropolis.
For four days, tens of thousands of Greeks had stood in line for hours to pay their respects to Christodoulos as he lay in state in the cathedral.
The archbishop headed the church for a decade, reinvigorating the vast institution.
He eased centuries of tension with the Vatican but angered liberal critics who viewed him as an attention-seeking reactionary who meddled in the affairs of state.
Giorgos Filias, professor of theology at Athens university, said: "What is important is that the church continues to attract young people and continue their open dialogue with other Orthodox Church. Any mistakes that were made were only human."
In 2001, Christodoulos received the late John Paul II, the first pope to visit Greece in nearly 1,300 years, despite vigorous protests from Orthodox zealots.
The archbishop followed up in 2006 with a historic visit to the Vatican.
A vocal opponent of issues ranging from homosexuality and globalisation to Turkey's efforts to join the European Union, the archbishop was regularly named Greece's most popular public figure.
No candidates have been declared for Christodoulos' succession.
Contenders are widely expected to include Metropolitan Bishops Anthimos of Thessaloniki and Hieronymos of Thebes, who both lost in 1998, when the church's Holy Synod elected Christodoulos as leader.