The proposal, announced on Thursday, is expected to strengthen competition, deliver more flights, and create more jobs.
Australian Airports Association chief executive Simon Westaway claimed that improved inbound tourism connections and sales and marketing visibility, along with necessary job safeguards, are expected to drive down airfares and benefit regional Australia.
"This deal is a major win for the aviation industry and the Australian flying public," he said.
Treasurer Jim Chalmers said the government approval came after the Treasury engaged in cross-government consultation, engaging the aviation industry, unions, and other relevant stakeholders to ensure the deal was in Australia's national interest.
Dr Chalmers said the proposal's approval was subject to legally enforceable conditions to ensure Australian representation on Virgin's board and protection of its customer data.
The airlines have also committed to a secondment program that will place 20 pilots and 40 cabin crew in Doha to gain long-haul flying experience, create backfill positions in Australia, and consult with unions specifically.
This follows a draft determination by the Australian Competition and Consumer Commission to allow the airlines to engage in cooperative conduct under an integrated alliance for five years, leading to 28 new weekly return services between Doha and Perth, Brisbane, Sydney and Melbourne.
"We welcome a new era for Virgin Australia," Virgin Australia Group chief executive Jayne Hrdlicka said.
"Qatar Airways' investment is a huge vote of confidence in our business and Australian aviation more broadly."
With AAP