Crowds carrying flags and chanting anti-Syrian slogans converged in central Beirut, turning the funeral into an impassioned political rally.
Security was tight, given Lebanon's current state of high tension.
Many Lebanese accuse Syria of involvement in Mr Gemayel's death, but Damascus rejects the claims.
The United Nations Security Council has agreed to a request from Lebanon to help investigate the murder.
The industry minister and Maronite Christian politician was shot in his car in a Christian area of Beirut on Tuesday.
LEBANESE ASSASSINATIONS
He was the fifth anti-Syrian Lebanese politician to be killed in two years, and his murder has intensified an acute political crisis in Lebanon.
Six pro-Syrian cabinet members have already resigned. The death or resignation of two more cabinet ministers would bring down the government.
US President George W Bush has pledged support for Lebanese independence from what he called the "encroachments of Iran and Syria".
'Shove civil war'
Troops and police ringed the cathedral where the Maronite Patriarch, Nasrallah Sfeir, conducted the funeral rites, calling on people not to take revenge for Mr Gemayel's death.
Foreign envoys joined the Gemayel family in the congregation, which greeted his coffin with applause.
The body of the 34-year-old politician was brought to the Beirut cathedral from his home village of Bikfaya, where he was to be buried later in the day.
KEY TERMS
Dozens of cars and buses had followed the cortege, waving the large white flags of the politician's right-wing Maronite Christian Phalange Party, and hooting their horns.
Posters also appeared showing the face of Syrian President Bashar al-Assad, with the slogan "Shove your civil war".
Speakers addressed the crowds after the service from a bullet-proof box.
The dead politician's father, former President Amin Gemayel, called for change in Lebanon, including a new president to replace pro-Syrian President Emile Lahoud.
"Let us promise ourselves and Lebanon that the second independence uprising started off today will not stop until it is completely realised," he said.
In a statement issued on Thursday, the Syrian government again strongly condemned Mr Gemayel's murder, which it said was "aimed at Lebanon's stability", and accused unnamed people of "exploiting the crime for personal ends".
Tribunal
Many Lebanese accuse Syria of involvement in the killing, which has sharpened tension between anti-Syrian forces, who back the government, and pro-Syrian groups like Hezbollah.
The UN commission already looking into the murder of ex-Lebanese PM Rafik Hariri in 2005 will take on the inquiry into Mr Gemayel's killing.
Correspondents say such a tribunal is highly controversial in Lebanon.
Pro-Syrian politicians are against it and it cannot begin to be set up until the Lebanese parliament votes for it.
In 2005, Syria withdrew its troops from Lebanon after a presence of 29 years, following massive domestic and international pressure following the assassination of Mr Hariri.
A recent UN report implicated Syria in the death, although Syria has denied involvement.
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