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.
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"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.