But the two-week pause on all India flights - including repatriations - leaves 9,000 Australian nationals trapped in the country, many of whom have been trying to get home for months already.
The restrictions come into effect from May 3 and breaching the ban risks civil penalties and up to five years imprisonment, Health Minister Greg Hunt said in a statement.
Mr Hunt made the unprecedented determination under the Biosecurity Act after receiving advice from Chief Medical Officer Paul Kelly.
"The risk assessment that informed the decision was based on the proportion of overseas travellers in quarantine in Australia who have acquired a COVID-19 infection in India".
Health Minister Mutahi Kagwe said Kenya had "observed the dire events in India. and resolved to suspend all passenger flights in and out of the country for a period of 14 days".
"The government should be looking for ways to safely quarantine Australians returning from India, instead of focusing their efforts on prison sentences and harsh punishments".
India has ordered its armed forces to help tackle the Covid crisis, as nations including Britain, Germany and the United States pledged urgent medical aid to try to contain an emergency overwhelming the country's hospitals.
'The government does not make these decisions lightly.
Penalties include five years jail or a $66,000 fine.
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"However, it is critical the integrity of the Australian public health and quarantine systems is protected and the number of Covid-19 cases in quarantine facilities is reduced to a manageable level".
More than 9000 Australians in India are registered as wanting to return, including 650 people registered as vulnerable.
"Our hearts go out to the people of India - and our Indian-Australian community", Mr Hunt said.
Some Australians, including cricketers Adam Zampa and Kane Richardson, took advantage of a loophole to return from India via Doha earlier this week.
India recorded 360,960 new infections in the last 24 hours, the largest in a single day taking the country's tally of infections to almost 18 million.
The ban will remain in place until at least May 15 - after which, Mr Hunt said, the aim was to resume repatriation and commercial flights as soon as possible.
The worsening Covid-19 crisis in India has spiralled in recent weeks.
India is now seeing a COVID-19 crisis as the second state with the largest number of detected COVID-19 cases in the world.
At that rate the country could see more than 30,000 deaths from coronavirus a day within a few weeks, but the country's poor record keeping means the true toll may never be known.