Prime Minister Scott Morrison on Friday announced the travel ban would end on its planned expiry date, following a fierce backlash against the harsh measures.
"All of this is about sensibly preventing a third wave of COVID-19 here in Australia," he told reporters in Sydney on Friday.
He said India was the world's most significant coronavirus hotspot for people wanting to travel to Australia.
There will be three flights this month to bring back the most urgent cases with 900 vulnerable citizens and permanent residents stranded in India.
All arrivals will be quarantined at the Northern Territory's Howard Springs mining camp where capacity is set to increase to 2000 beds.
People found to have coronavirus in a pre-flight test will be denied the right to board planes.
"That is a clear port of entry requirement. We will be holding the line on that," Mr Morrison said.
Up to 200 passengers could be on the first flight, which will depart on May 15. But the 9000 Australians still stuck in India could face months of waiting to return home, with the Asian nation in the grips of a coronavirus catastrophe.
One repatriation flight is due to arrive every seven to nine days, with an estimated 1000 Australians returning by the end of June.
The number of people with coronavirus at Howard Springs has fallen to 21 from more than 50 a week ago, while there is expected to be no cases linked to Indian repatriation flights by next Friday.
India recorded another grim global world record on Thursday, with more than 412,000 new coronavirus cases and almost 4000 deaths.
Mr Morrison said the government did not know how many of the stranded Australians had contracted the disease.
Cabinet's national security committee signed off on the decision on Thursday following advice from Chief Medical Officer Paul Kelly.
Mr Morrison chaired Friday's national cabinet meeting of state and territory leaders who were briefed on the pause ending.
NSW and Queensland agreed to receive more repatriation flights.
The controversial ban came under heavy fire from within conservative ranks, the Indian-Australian community and human rights groups after the government threatened jail and fines for people who tried to circumvent it.
The government argued it was necessary to ease pressure on quarantine and prevent a third wave breaking out in Australia.
Talks are underway with Sri Lanka on ensuring pre-flight testing as cases rise on the island nation to India's south.
Mr Morrison also announced national cabinet would revert to monthly meetings just three weeks after requesting state and territory leaders convene twice every seven days.
The meeting schedule was increased amid problems with the vaccination rollout which has now passed 2.5 million doses.