Acting Health Minister James Merlino announced some services will restart from Thursday, with hospitals scaling up their operations to enable procedures to resume from 11.59pm on Tuesday.
IVF clinics were contacted by authorities earlier this month and asked to cancel some appointments as part of a pause on elective surgeries in response to the rising number COVID-19 hospitalisations.
The most time-critical IVF procedures for patients such as couples whose eggs were about to expire and women who took pre-cycle medication before January 6 were still able to go ahead.
The move attracted criticism from Prime Minister Scott Morrison and prospective parents, while Victorian Opposition Leader Matthew Guy described it as "cruel and heartless".
An online petition to reinstate fertility and IVF treatments garnered almost 140,000 signatures.
Mr Merlino said he received advice from the chief health officer that restrictions on IVF procedures can be removed, given the "specialist nature of the workforce and the facilities and equipment used are not imperative to support the pandemic response at this time".
The health department will work with the Royal Women's Hospital to prioritise urgent patients, ensuring the changes do not affect the COVID-19 response in that hospital.
"IVF is a challenging journey for anyone to go through, let alone in the midst of a global pandemic, and we're deeply sorry for the distress caused," Mr Merlino said.
Premier Daniel Andrews also apologised for the distress caused by the pause at a press conference on Thursday.
"I just want everyone to know across the community, everyone's doing their very best just to keep people safe. That's what drives us," he said.
He said the pause was based on "very, very conservative" advice provided to the government by health authorities, which is currently under review.
"There's a process going on at the moment to review the advice and a number of other day surgery and day procedures. So hopefully, I can make some announcements next week to add to that list," Mr Andrews said.
Melbourne IVF Medical Director Fleur Cattrall welcomed the reversal.
"We are relieved that the ban has been lifted today; a continued ban for many months would sadly have meant some Victorians would miss out completely on having a baby," she said in a statement to AAP.
"We believe resuming IVF treatment is the right thing to do, and it can continue in a COVID safe manner and without impacting on the current public health response to the pandemic."
Dr Cattrall said the fertility provider had already begun contacting patients to resume treatment.
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