Aljazeera's correspondent in the Lebanese capital, Mia Baydun, reported hearing two loud explosions within five minutes of each other over the southern part of the city.
The noises were apparently supersonic booms of Israeli warplanes breaking the sound barrier about 7:10 pm(1610 GMT).
It caused panic in the city and drew Lebanese anti-aircraft fire in the direction of the planes.
An Israeli military source said the overflights were "a message to the government of Lebanon" to better control the southern border area.
Also on Tuesday, two Israeli soldiers and a Hizb Allah man were killed in southern Lebanon.
UN envoy in Lebanon requested to hold consultations "on the possibility of calling a special Security Council meeting to condemn the Israeli aggressions"
Lebanese Foreign Minister
The violence erupted a day after a Hizb Allah leader, Ghalib Awwali, was killed by a car bomb in front of his home in the southern suburbs of Beirut.
The Lebanese government held Israel responsible for the attack.
Lebanon said it was considering a protest to the United Nations over what it called "aggressions" by Israel on its soil, while Hizb Allah warned it would avenge the killing of a second member in two days.
Hizb Allah chief Shaikh Sayyid Hasan Nasr Allah vowed to "cut the hand" of Israel on Monday after blaming it for the death of Awali.
Beirut says Israel has been trying to regain lost ground by conducting illegal incursuions into Lebanon since its May 2000 withdrawal from the south.
Israeli army captain Jacob Dallal defended Israel's entry into Lebanon.
"There was a deliberate attack by Hizb Allah snipers on a Tshahal (army) position in the western area of the border. Two soldiers have been killed," he said.
"The army has responded to the shooting."
Israel Radio identified the dead as an army radio technician and a military intelligence soldier who were repairing an antenna at the outpost.
After the incident, Israeli helicopter gunships crossed into Lebanese territory and fired eight rockets into the villages of Aita Shaab and Balat, apparently targeting Hizb Allah.
The Lebanese group announced on its al-Manar TV station that one of its members was killed after his observation post was hit by Israeli tank fire, which it described as the cause of the clashes in the area.
Lebanon has accused Israel of
violating the UN-drawn blueline
Lebanon said Israel is engaging in hostile acts that violate the UN-drawn Blue Line demarcating the border, and that it is considering calling on the UN Security Council to act.
"There is a real risk of escalation and regional destabilisation" if the situation remains unchecked, a foreign diplomat in Beirut said.
Lebanese Foreign Minister Jean Obeid told the country's UN envoy to hold consultations "on the possibility of calling a special Security Council meeting to condemn the Israeli aggressions", according to ministry officials.
Lebanese police said Israeli helicopter gunships and jets crossed the border region on Tuesday and Hizb Allah retaliated with anti-aircraft fire.
The Israeli strikes resulted in a number of fires in the region, police said.
A statement issued by Hizb Allah said, "We will choose the suitable time and place for a deterrent response that will make the enemy understand that any aggression against our people ... will be very costly."
Lebanese President Emile Lahoud called the killing of Awwali a flagrant aggression by Israel while Prime Minister Rafiq Hariri said he was confident the criminals would be arrested and given the punishment they deserved.
Hizb Allah was instrumental in the May 2000 Israeli military pullout from southern Lebanon after an occupation lasting 22 years.