Tuesday's clashes marked the worst violence to grip Beirut since May 2008, when 100 people were killed in battles between supporters of a Hezbollah-led alliance and those of Lebanon's pro-Western Sunni prime minister, Saad Hariri.
An army spokesman told AFP the situation was calm on Wednesday afternoon, although tanks and foot patrols could be seen across the capital throughout the day.
Bullet casings and broken glass covered Burj Abi Haidar streets on the morning after, as shopkeepers swept away rubble from their stores and most residents stayed indoors. Cars parked nearby were also badly damaged.
Supporters of the two movements used shoulder-fired rocket-propelled grenades and machine-guns in four hours of fighting that erupted at about 7 pm (1600 GMT) Tuesday and also left 11 people wounded.
Two of the dead were identified as Hezbollah members Mohammed Fawaz -- the party's representative in Burj Abi Haidar -- and Ali Jawad. The third was named as Ahmed Omayrat of Al-Ahbash.
Jawad was buried in his hometown of Kfar Fila in southern Lebanon and Omayrat was buried in Burj Abi Haidar on Wednesday afternoon. Fawaz's funeral is planned for Thursday.
Witnesses said the clash began as an argument between Fawaz and supporters of the Sunni group over a parking space near a mosque popular among Al-Ahbash.
The violence broke out at around the time of "iftar," the meal that breaks the dawn-to-dusk fast observed by the Muslim faithful during the holy month of Ramadan.
In northern Lebanon, a 26-year-old woman was wounded overnight as two grenade explosions shook the port city of Tripoli, just hours after the clash in Beirut, a security official told AFP. The woman was in a stable condition.
Hezbollah and Al-Ahbash, which describes itself as a charity promoting Islamic culture, said in a joint statement that Tuesday's "regrettable incident was isolated and did not have any political or confessional basis."
The Lebanese press on Wednesday expressed surprise the latest round of violence pitted supporters of two groups with similar political views against each other.
"The use of medium-range weapons in religious centres, shops and homes shows that the pot is ready to boil over at any moment, even if the incident was described as personal," warned An-Nahar, a daily close to Hariri's bloc.
Hezbollah, Lebanon's most powerful political and military force, is backed by Syria and Iran, while Hariri's alliance is backed by Saudi Arabia and the United States.
Al-Ahbash emerged in 1983 and gathered strength during Syria's military deployment in Lebanon, which ended under international pressure after the 2005 murder of Hairi's father, ex-premier Rafiq Hariri.
The movement has since lost considerable weight.