German President Horst Koehler, French Interior Minister Nicolas Sarkozy and the Romanian secretary of state for religions, Adrian Lameni, were among those present at the service celebrated by Cardinal Walter Kasper, the Vatican's top ecumenical official.
It was held at the Taize Ecumenical Community's Church of Reconciliation where 90-year-old Brother Roger was killed a week ago, his throat slit allegedly by a woman from Romania who surged from a crowd of 2,500 attending a prayer service.
Opening the funeral service, Brother Alois, a 51-year-old German Roman Catholic appointed to succeed Taize's leader, asked that God forgive Brother Roger's killer "who knew not what she did."
The 36-year-old suspect has been placed under formal investigation for premeditated murder, a step short of being charged. The media in Romania has identified her as Luminita Solcan, from the northeast city of Iasi, and quoted local officials as saying she had suffered mental instability.
Some mourners held white candles, and many reached out to touch the coffin as it was carried from the church by white-robed monks.
Brother Roger, known worldwide for his work to develop dialogue and unity among all Christians, was buried in the local cemetery of the village of Taize where he has lived since 1940.
The funeral service was retransmitted on a giant screen outside the community's church where thousands gathered in a light rain. Several hundred people returning from the World Youth Day Festival in Cologne, Germany, hummed meditative chants as they waited for the service to start.
"It's the end of a myth. He was so charismatic," said Mathilde Fouard, 20, who traveled from Grenoble for the funeral. "I came to say goodbye one last time and to bring him grace in my prayers."
The suspect rushed from the congregation of some 2,500 and plunged a knife into Brother Roger's throat at the start of the Aug. 16 service.
Brother Roger Schutz was born to a Swiss Protestant father and a French Catholic mother. He moved to Taize in 1940 with plans to found a monastery.
He harbored Jewish refugees during the World War II Nazi occupation of France, then built the Taize Ecumenical Community with a mission to reconcile all denominations of Christians and promote dialogue and peace.
Brother Roger was deeply respected in the Roman Catholic Church, the Church of England and by Christian leaders who praised his contribution to Christian unity.
The Taize community, which the late Pope John Paul II visited in 1986, draws some 100,000 people each year for prayer and meditation.
"The death of Brother Roger has touched us," said Henri Catherin, 76. "Once again, it is an artisan of peace killed in violence."