Mourners marched to the Greek Orthodox Church of Saint George in the Lebanese capital, Beirut, where there were emotional scenes.
Supporters waved Lebanese mourners flags swarmed the streets of Beirut, venting their rage at the pro-Syrian President Emile Lahoud.
"Lahoud, shame on you. Resign," they chanted. "Our president is under the Syrian boot," and "Syria Out."
Damascus has denied any involvement in the murder on Monday.
Mr Tueni had only just returned from France where he had spent some time in fear of his life amid a spate of attacks on critics of Syria.
He is the second high profile opponent of Syria to be killed, following the assassination of former Prime Minister Rafik Hariri in February.
Hundreds of army commandos and police forces were deployed in Beirut as schools, banks and shops remained shut.
Hariri probe
Damascus is under pressure to comply unconditionally with a United Nations probe into the murder of Mr Hariri.
The UN Security Council has been considering a draft resolution by France to extend the investigation.
The chief UN investigator, Detlev Mehlis, said his findings so far had reinforced earlier conclusions that Syria and Lebanese intelligence were involved in the attack.
The 48 year old was killed in a massive car bomb blast Monday, along with his driver.
Emotional funeral
At the emotionally charged funeral, Mr Tueni's father, veteran diplomat
Ghassan Tueni urged the Lebanese to rally around his son's quest for Lebanese sovereignty and unity among Christians and Muslims.
"Bury with Gibran any sentiment of revenge and your rancour," said a stoic Mr Tueni, one of the few mourners who remained dry-eyed throughout the ceremony.
They packed into the white stone 19th century St George’s Cathedral as it rang out with Greek Orthodox chants and echoed with the sobs of his widow Siham, his daughters Nayla and Michelle, family members, colleagues, politicians and supporters.
During his burial at the Mar Mitr cemetery, his daughter Nayla collapsed amid the sea of mourners and had to be assisted by the civil defence.
Ferocious hostility for Syria, which many Lebanese blame for a series of political assassinations over the years, was visible on banners held high over the heads of mourners inside and outside the cemetery.
In these charged conditions, Arab League Secretary General Amr Mussa arrived in Beirut on a fence-mending mission saying he "cannot watch and let the situation deteriorate between Lebanon and Syria and reach an explosive level".
"I am on an urgent diplomatic mission to defuse the dangerous situation" between Beirut and Damascus, Mr Mussa told reporters, after talks with Lebanese Prime Minister Fuad Siniora.
He travels Thursday to Damascus.
In parliament, several Lebanese lawmakers lambasted Syria and demanded a government change in Damascus after observing a minute of silence in homage to Mr Tueni, whose seat was draped in a Lebanese flag.