The Australian Competition and Consumer Commission said it thought the benefits of the alliance outweighed the drawbacks.
"The ACCC is satisfied that the alliance is likely to result in material, but not substantial, public benefits," ACCC chairman Rod Sims said.
The alliance, agreed last year, will see the two collaborate on pricing, sales and flight scheduling and is seen as key to Qantas' attempts to turn around its loss-making international operations.
"Qantas is an Australian icon and the future of its international business is much brighter with this partnership," said Alan Joyce, chief executive of Qantas.
"Customers are already responding very strongly to the joint network that Qantas and Emirates have built, and to the frequent flyer benefits that extend across it, with a significant increase in bookings."
The ACCC had already given the tie-up interim approval, allowing the two carriers to begin selling codeshare flights between Australia and Europe, North Africa, the Middle East and Asia.
Wednesday's final ruling, which lasts for just five years, will also allow Qantas and Emirates to pair up on flights across the Tasman, subject to conditions.
Under the partnership, Qantas will use Dubai, rather than Singapore, as the carrier's stopover point for its flights to London.
The first Qantas flight to London via Dubai departs on Sunday, March 31.
Image: © Getty
Copyright is owned by Asia Outlook and/or Outlook Publishing. All rights reserved.