The clashes, between Sunni pro- and anti-Syrian groups, followed the shooting dead on Sunday of two anti-Syrian clerics.
The violence is the first in Beirut since the conflict began in neighbouring Syria in March last year.
The BBC's Jim Muir in Beirut says the incident shows how divided the Lebanese are over the Syrian crisis.
It follows a week of clashes in the northern city of Tripoli between anti-Syrian Sunnis and Alawites who support the regime of Syrian President Bashar al-Assad.
Syrian and Lebanese politics have been deeply intertwined throughout the history of the two states.
Syria, the dominant partner, had a large military presence in Lebanon for 29 years, finally withdrawing soldiers in 2005, but maintaining a strong influence. Political factions in Lebanon have often defined themselves as pro- or anti-Syrian.
By Jim MuirBBC News, Beirut
Given how deeply and sharply Lebanon is divided over Syria, it's a miracle that there hasn't been much more violence than there has.
But the killing of two Sunni clerics at a Lebanese Army checkpoint in the north of the country on Sunday could hardly pass without consequence - though the fallout could have been much greater.
Only in Beirut did the tension break into open conflict. And it was restricted to a clash between Sunni groups, with the mainstream Future faction of Saad al-Hariri using the occasion to squeeze out the small, pro-Syrian Arab Movement Party, whose leader Shaker Berjawi fled.
In nearby areas of south Beirut, Hezbollah - the most powerful force in the land - kept well out of it.
Political and religious leaders from all sides urged restraint, while the government pledged a vigorous enquiry into the death of the two shaikhs.
Divisions over Syria are the defining issue in Lebanese politics. Everybody knows how real the danger is that the country would be torn apart if those differences are allowed to erupt freely onto the streets.
Sunday's violence was triggered by the shooting dead of two Sunni sheikhs linked to the anti-Syrian Future movement, headed by opposition leader Saad al-Hariri, at a Lebanese army checkpoint in the north on Sunday.
Supporters of Mr Hariri responded by blocking main roads with burning car tyres, but security forces intervened to clear them.
In Beirut's southern district of Tariq al-Jadideh, offices of a local pro-Syrian leader came under attack by gunmen.
Rocket-propelled grenades and machine-gun fire were heard for much of the night.
But the clashes died away after the leader, Shaker Berjawi, left the area, and the Lebanese Army moved in.
Sunni religious and political leaders have called for the utmost restraint, and an investigation has been launched into the killing of the two sheikhs.
Correspondents say there are fears of a return to the violence seen in clashes between Sunni and Shia Muslims in 2008 which brought the country close to civil war.
At least two people have been killed and 18 injured in clashes overnight in the Lebanese capital Beirut.