The crowd in Martyrs' Square on Friday held photos of the prominent anti-Syrian journalist and raised black pens to symbolise freedom of expression. At the end of the hourlong protest, they sang the national anthem.
Kassir was killed inside his car at midmorning on Thursday in the Christian Beirut neighbourhood of Ashrafieh, where he lived. The bomb set the car ablaze and shattered windows in nearby buildings.
The opposition accused Syria of interfering in Lebanon's politics and called for a general strike on Friday.
An-Nahar newspaper, for which Kassir was a columnist, staged the silent protest 200 metres from its office building.
Kassir was killed in a bomb blast
in Beirut on Thursday
Many schools closed, while others suspended classes. But the call for a widespread strike came too late for many people to heed. Only a handful of shops were closed in Ashrafieh.
Kassir, 45 and a Christian, was a university professor and founding member of the Democratic Left Movement, a small group that joined the anti-Syrian opposition and played an active role in the protest campaign against Damascus's control.
He wrote a column in An-Nahar, a leading newspaper that frequently criticises Syria, and was a regular on TV talk shows.
In a recent television appearance, he said he had long received threats by security agents trying to silence him.
Interior Minister Hassan Sabei said initial reports indicated the bomb that killed Kassir was placed under the car and detonated by remote control.
Prime Minister Najib Mikati vowed that his government "will not allow anyone to target security and freedom".
Giselle Khoury, Kassir's wife, demanded an international investigation into her husband's death. Khoury, a journalist, was in the United States at the time of the explosion.
Kassir will be buried in Beirut on Saturday.
The bombing came as an international team headed by German prosecutor Detlev Mehlis was investigating the February assassination of former Prime Minister Rafiq al-Hariri, whose death led to the ouster of Syrian troops after nearly three decades in Lebanon.
Giselle Khoury, Kassir's widow, has
demanded an investigation
Mehlis met on Friday with President Emile Lahoud, who expressed hope that the team would also investigate Kassir's murder, saying the government would discuss that possibility with the United Nations.
According to a statement issued by his office, Lahoud told Mehlis that the two killings were related and aimed at destabilising the country.
Anti-Syrian leaders also were quick to make a link between the two killings and reiterated calls for the resignation of Lahoud, a Syrian ally.
Al-Hariri's son and political heir, Saad al-Hariri, said the same people were behind both assassinations, "and God knows what's coming".
"We will not be afraid. ... We want our freedom, we want our independence, we want our sovereignty and no one is going to stop us," a defiant al-Hariri told reporters on Thursday.
Kassir's death came ahead of Sunday's second round of parliamentary elections - a ballot the anti-Syrian opposition hopes to win and end Damascus' control of the legislature.
Syria denied it was behind Kassir's killing and stressed its determination not to interfere in internal Lebanese affairs.
In Washington, US Secretary of State Condoleezza Rice condemned Kassir's killing as a "heinous act". Visiting EU foreign policy chief Javier Solana said it was a tragedy, adding that Kassir was "a very honest man".