Schools and businesses closed as crowds gathered outside the glass tower in Beirut housing Tueni's right-leaning al-Nahar daily, which was adorned with a huge banner depicting the slain journalist.
Youths from Christian and Sunni Muslim political parties angrily chanted anti-Syrian slogans, while others clapped slowly in a sign of respect.
Tearful women wore black while other demonstrators carried flags and pictures of civil war-era political leaders.
The mourners moved on to the nearby St. George's Cathedral for the funeral. Tueni was buried in the Mar Mitr neighbourhood in east Beirut.
A car bomb killed Tueni on Monday
(Photo: Christian Henderson)
Police, who wouldn't speak on the record, estimated the crowd at more than 100,000, The Associated Press said.
But some other witnesses and observers, and police unoffically, said they thought it could be as high as 200,000.
Lebanon has been plunged into renewed crisis by the killing of Tueni.
Many had believed that the period of assassinations and car bombings that struck Lebanon after the killing of former premier Rafiq al-Hariri in February had passed.
However, Monday's blast signals a return to the killings, and those attending the funeral wondered aloud who will be next.
"People are going to be afraid. Nobody is going to be outspoken after this. Jebran was really outspoken," said 32-year-old Raid, who declined to give his full name.
"We don't understand what they want," said Marwan Hanna, 31, in reference to those responsible for the attacks. "What do they want? Do they want to kill us progressively? Do they want to shut us down? We do not understand."
Tueni was one of the strongest critics of Syrian involvement in Lebanon. In 2000 he broke a taboo by writing an editorial condemning Syrian presence in Lebanon.
In the anti-Syrian demonstrations in spring this year, Tueni emerged as a firebrand speaker who captured the imagination of the mostly young activists who took part in the protests.
Many feel his death has left a large gap in the movement that emerged out of these demonstrations.
"It's clear they killed him because he was a young dynamic person," said 32-year-old Joanne El-Mir.
"They killed three people at the same time: a journalist, MP and a leader of the spring revolution," she said.
"What do they want? Do they want to kill us progressively? Do they want to shut us down? We do not understand"
Marwan Hanna, 31-year-old mourner
Joe Saadeh, standing with a friend carrying a flag of a Christian party, said: "He was fighting with his pen not with his gun. He used his word to fight."
In a country where religious divides run deep, Tueni was considered by many to be a rare leader who rose above sectarian politics.
"Jebran was one person who was a leader of the whole country - he had nothing to do with religion," said mourner Chady Abdullah.
Amid the collective mourning, there were telltale signs of how divided Lebanon remained.
Lebanon's Shia parties Hizb Allah and Amal walked out of the government on Monday after the cabinet voted for an international investigation into Tueni's killing, and the two groups' party flags were absent from the funeral.