A doctor at the Sainte Therese hospital, Georges Karam, confirmed that two died from wounds to the neck while the third victim was shot in the stomach.
Security sources said soldiers opened fire when protesters began throwing stones on Thursday, angry over soaring fuel prices.
Two military vehicles were also damaged in the skirmish around the mainly Shia Muslim Hay al-Silum suburb.
Trade unions had called for a general strike to protest against the rise of fuel prices and the economic policies of the government of Prime Minister Rafiq Hariri.
Fuel price rage
Widespread anger at petrol prices has apparently bolstered support for Thursday's strike, with some estimating half a million protesters across the country.
Over the last several days, most labour unions and associations announced that they would participate in the strike, while shops and private businesses in the capital were preparing to close.
Meanwhile, Hariri has urged Justice Minister Bahij Tabbarah and the public prosecutor's office to take action against petrol stations for failing to comply with last week's cabinet decision to lower prices.
Petrol prices are currently around $0.80 a litre, while the government has demanded a charge of $0.74.