Frontline workers including pilots, cabin crew and airport staff must be fully vaccinated by mid-November.
The company says its remaining employees have until the end of March next year to receive both doses.
It comes as the state of New South Wales reported its biggest daily rise in coronavirus infections.
The Australian flag carrier is the country's biggest, most high-profile company to introduce a mandatory vaccination policy.
"We provide an essential service, so this will help guard against the disruptions that can be caused by just one positive COVID-case shutting down a freight facility or airport terminal," Qantas chief executive Alan Joyce said in a statement.
"It's clear that vaccinations are the only way to end the cycle of lockdowns and border closures and for a lot of Qantas and Jetstar employees that means getting back to work again," he added.
Qantas said that a poll of its 22,000 staff found that 89% of respondents had already been vaccinated or were planning to be and around three-quarters of them thought it should be mandatory.
It said that 4% of the almost 12,000 who responded - around 480 staff - were unwilling or unable to get the vaccine.
The airline said that staff with documented medical reasons for not being able to be vaccinated would be given an exemption.