The final two flights from Lebanon to Cyprus left on Sunday carrying 422 passengers.
The Department of Foreign Affairs and Trade said 3170 citizens, permanent residents and their family had left Lebanon across 18 government flights since October 5.
It comes as a further 147 people returned home to Australia from Cyprus on Sunday night, with 2552 citizens and family members having touched down on Australian soil.
A Qatar Airways flight is due to land in Sydney on Monday carrying more returning to Australia.
A further flight is also scheduled for Tuesday.
While no more government-assisted flights will be running out of Lebanon, those in the region have still been urged to return to Australia.
"Our message to Australians in Lebanon remains – now is the time to leave," a Department of Foreign Affairs spokeswoman said.
"Commercial flights remain available, and Australians should take the first flight option that is available to them.
"The Australian government thanks partners and commercial airlines for their assistance to bring Australians safely home from Lebanon through assisted departure flights."
Pro-Palestine crowds rallied in Brisbane on the weekend.
The flights followed an escalation in Israel's ongoing conflict with the Lebanese militant group Hezbollah in recent weeks, with a campaign of intense bombings across Lebanon including its capital Beirut.
More than 2200 people have been killed and another 1.2 million have been displaced across a nation about the size of Greater Sydney.
It comes as thousands of people have marched to protest "the expanded genocide" in the Middle East and call on the Australian government to "do better for Palestine".
A large crowd gathered at Queens Gardens, in Brisbane, on Sunday to hear 10 speakers demand an "end to Israel's genocide in Gaza, to the apartheid occupation of Palestine, and to Israel's assaults on Lebanon and the West Bank".
Organisers Justice for Palestine Magan-djin called the peaceful protest to "honour the victims of the expanded genocide and Labor's complicity".
Queensland Greens candidate for Moreton, Remah Naji, invited a 10-year-old boy named Raza to the stage to talk about the horror of seeing children killed in the widening conflict.
"I want to share all of what I have witnessed in just the past year," he told the crowd, while other speakers cried as they recalled family members who had died in Gaza.
A peaceful protest was held in Brisbane as the government wound down assisted flights from Lebanon. (Jono Searle/AAP PHOTOS)
Chants synonymous with pro-Palestine protests across the world were heard including "ceasefire now" and "from the river to the sea, Palestine will be free" as well as "always was, always will be Aboriginal land".
The full length of Victoria Bridge was awash with protesters as many of those gathered then marched through the city centre to the ABC's headquarters at South Bank to urge "fair and just media coverage of the atrocities".
Some carried Palestinian flags, others Lebanese flags in response to the ongoing Israeli military assault in Lebanon.
International leaders have raised their concerns at the intensified conflict between Israeli forces and Hezbollah after three United Nations peacekeepers were wounded when Israeli strikes shook the main base in southern Lebanon in recent days.
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