At least 10 cars were destroyed, some tossed into a valley in the hilly al-Mukhallis area when a car bomb exploded as Tueni's convoy passed through the area on Monday.
Aljazeera's correspondent in Beirut, Abbas Nasir, said that Lebanese security forces had confirmed the targeted car belonged to Tueni and that only three people had been killed. Earlier reports stated that four had died.
Lebanese security forces, officials and Tueni's relatives have converged on the blast site, Nasir said.
Tueni was married, with four daughters.
The area is an eastern Christian suburb a few kilometres from the headquarters of the UN team investigating the assassination of former prime minister Rafiq al-Hariri.
One of the other two killed was Niqola Fluti, a Tueni guard, sources close to the member of parliament told Aljazeera. The identity of the third victim was not immediately known.
Prime Minister Fuad Siniora called an emergency meeting of top security officials and asked the Cabinet to convene later on Monday.
Preliminary estimates put the bomb's size at 40kg (88lb) of TNT.
Lebanese Druze leader Walid Jumblatt all but openly accused Syria of assassinating Tueni.
"We have received the message of the new assassination from the nearby security regime, as Mehlis presents his final report on al-Hariri's assassination to the UN Security Council," he told Aljazeera in an interview.
In an interview broadcast on Russian television on Sunday, Syrian President Bashar al-Assad reiterated his country's innocence and said any attempt to impose sanctions against Syria would destabilise the region.
"This regime has killed al-Hariri, assassinated Samir al-Qasir and George Hawi. We have received the message," said Jumblatt, the leader of the Progressive Socialist Party.
Tueni said in August he was at
the top of an assassination list
"I have heard President al-Assad ... say that imposing sanctions on Syria will cause instability in the area," Jumblatt said. "We have received the message. Thank you. However, we will continue calling for the truth no matter what the price."
A former Lebanese official countered Jumblatt's accusations.
"How would Syria benefit from assassinating Jebran Tueni at this particular point of time?" Wiam Wahab, a former minister, told Aljazeera.
"Syria is not that stupid to assassinate him a few hours before the UN Security Council holds a meeting to discuss Mehlis's report."
Tueni had spent much of his time since August outside Lebanon, citing security fears. He was believed to have returned to Beirut late on Sunday.
"Lebanese officials received accurate information from the international investigation committee about an assassination list of several politicians," he told the Arabic-language Radio Orient in Paris in August. "My name is on top of this list."
Tueni's uncle, Druze Telecommunications Minister Marwan Hamadeh, survived an attempt on his life in 2004.
Tueni's death has removed one
of Syria's harshest political critics
Tueni was publisher, chairman of the board and general manager of Lebanon's leading newspaper Al-Nahar. A columnist at the daily, Samir Kassir, who also criticised Syrian policies, was killed by a bomb in his car in June.
Tueni's grandfather, also Jebran Tueni, founded Al-Nahar. His father Ghassan Tueni is considered the dean of the Lebanese press, having turned the newspaper into an institution respected by friend and foe across the Arab world.
Lebanon has been rocked by a series of explosions targeting anti-Syrians in recent months. Media reports have linked the bombings to the investigation into al-Hariri's assassination as an attempt to derail the inquiry.
The explosion on Monday came hours after chief UN investigator Detlev Mehlis submitted his report to UN Secretary-General Kofi Annan on the investigation.
Jumblatt: This assassination is a
message to Lebanese journalism
Druze MP Jumblatt told Aljazeera Tueni was targeted as he represented a free voice.
"Al-Nahar newspaper was and will always be the voice of the free people in Lebanon. Al-Nahar will always remain a free voice despite the assassination of Tueni," he said.
"This [assassination] is a message to Lebanese journalism.
"However, Lebanese journalism and the free people are much stronger than the terrorist regime that has sent these messages," Jumblatt said.
Tueni is considered by many Lebanese to be the most high-profile figure to have been killed since al-Hariri's assassination.
"To give you a sense of magnitude, with all 15 assassination attempts Gebran was only second to Hariri and the reason for this was his unique bravery"
Lawyer and presidential candidate
Chibli Mallat, a lawyer and presidential candidate, said: "To give you a sense of magnitude, with all 15 assassination attempts Gebran was only second to al-Hariri and the reason for this was his unique bravery.
"He broke the taboo four years ago with an editorial against the Syrian presence which was taken up internationally," he said.
Mallat added that the UN Security Council should establish an international tribunal to punish those responsible for the killings.
Nadim Shehadi, head of the Centre for Lebanese Studies at Oxford University, said the killing would continue to create a state of fear and uncertainty in Lebanon.
"It's spreading an atmosphere of terror and it works. It is on everybody's mind," he said.
*Christian Henderson in Beirut contributed to this report.