From Monday, flights will resume to Sydney, while services will return to Melbourne from Tuesday and to Brisbane from Thursday.
Passenger flights between Dubai and Perth, as well as cargo operations to all Australian points, continue as scheduled.
Hundreds of Australians were last week left stranded after the major airline announced the cancellation on Friday night.
"We regret the inconvenience caused to our customers in the period where we had to temporarily suspend our services," a statement distributed by the airline read.
"The pandemic has made international flying incredibly challenging, and the dynamic restrictions and requirements implemented by the different state authorities in Australia had added complexity and burden to our operations.
"This led us to temporarily suspend passenger services while we engaged with various stakeholders regarding crew protocols and other operational details."
Emirates confirmed crew operating on Australian flights were already mandated to take a PCR coronavirus test 48 hours prior to scheduled flight departure times from Dubai.
"With the latest adjustments, these tests will be administered in their homes, and our crew will also observe self-quarantine in their homes from the moment of testing until their flight."
"This is an added burden for our crew as individuals, for our rostering, and operating costs, and therefore this decision was made after careful review and consideration.
"We are grateful that our wonderful crew teams are very understanding and supportive, which has enabled us to quickly restart passenger services.
"The safety of our customers and colleagues is always our top priority, and as always, we work closely with the authorities and health experts in this regard."