The Egyptian diplomat, who became the first African secretary-general in 1992, died in Cairo on Tuesday aged 93.
He was given an elaborate military send-off attended by President Abdel Fattah al-Sisi.
The ceremony in a prominent Cairo mosque was also attended by Sheikh Ahmed al-Tayib, the head of Sunni Islam's seat of learning, Al-Azhar, and Coptic Pope Tawadros II.
Boutros-Ghali's coffin, draped in the Egyptian flag, was later carried to the city's main cathedral for a Christian service led by the pope and attended by Egyptian, European and African diplomats.
"Egypt has lost one of its symbols, one of its best leaders, an example of patriotism," Amr Mussa, former head of the Arab League, told mourners.
Boutros-Ghali's tenure as UN chief began in 1992 but ended abruptly in 1996 when the United States vetoed his second term.
Following his death on Tuesday, UN Secretary-General Ban Ki-moon described Boutros-Ghali as a respected statesman and scholar of international law who brought "formidable experience and intellectual power" to the top UN job.
After a series of clashes with the US administration, Washington turned against Boutros-Ghali and decided to back Ghanaian Kofi Annan for the top post in late 1996.
Under Boutros-Ghali's tenure, the United Nations expanded its peacekeeping missions but a retreat from Rwanda ahead of the 1994 genocide and from the Bosnian enclave of Srebrenica a year later were seen as dismal failures.
Relations with the United States began to sour in late 1993, when a US-led operation in Somalia led to major casualties among American troops.
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