Both the United Nations and France, which commands the UN peacekeeping force overseeing the UN-brokered truce, have called on Israel to halt the overflights, which they say violate the ceasefire.
The overflights began early on Tuesday morning, concentrated over the capital's impoverished Shia southern suburbs left devastated by Israel's summer war with the resistance group Hezbollah, and lasted around 45 minutes.
In the south, where the peacekeeping force is policing UN Resolution 1701, the ceasefire resolution that came into force on August 14, the warplanes also carried out low-altitude mock raids, local security forces said.
A number of aircraft also made sonic booms over the southern port city of Tyre, witnesses reported.
An Israeli military spokesman in Tel Aviv declined to comment on the overflights.
"We do not elaborate on operational activity," he said.
A statement released in the name of Geir Pedersen, the UN special envoy, condemned the persistent violations of Lebanese air space.
"Pedersen expresses his serious concern at the continuing overflights by Israel which constitute a breach of Lebanese sovereignty and specifically of Security Council Resolution 1701," it said.
"The UN interim force in Lebanon has reported some eight air violations over the past two days which they have observed over their area of operation."
France also condemned the overflights.
"We consider them contrary to the spirit and the letter of Resolution 1701," a foreign ministry spokesman said.
Amir Peretz, the Israeli defence minister, has insisted that the overflights will continue until Hezbollah fighters halt what he says is arms smuggling in defiance of the UN resolution.