Hezbollah and Amal have been locked in a power struggle for more than a year with the government of Fouad Siniora, the prime minister.
The deadlock has fuelled sectarian tensions between Shia Muslims loyal to the opposition Hezbollah and Amal factions, and Sunni supporters of Saad al-Hariri, who leads the governing March 14 coalition.
Amal, which is led by Nabih Berri, the parliament speaker, called on its followers to halt the protests.
"We have no link to this action. We call on people not to react. We call on them to pull out of the streets," Ali Hassan Khalil, a senior Amal official, told the Reuters agency.
Hezbollah members used loudspeakers to urge calm.
The violence escalated after an Amal activist was shot dead when the army moved to break up a demonstration against power cuts.
Opposition supporters say their strongholds are unfairly targeted by electricity-rationing practices.
The Lebanese army, seen as neutral in the crisis, had fired in the air to disperse the initial protest. It said it was investigating who was behind the shooting, which it said killed two people.
Heavy gunfire was heard and fighters were seen in nearby Shia Muslim and Christian streets.
Cars were set ablaze in Beirut and protests spread beyond the capital to Shia villages in the south and the Bekaa Valley to the east.
Protesters used blazing tyres to block several main roads, including the highway to the airport.
One of those killed was Ali Hassan Hamza, a member of Amal.