Michelle Kenney had her medical licence suspended in May after Hampton Park Women's Clinic was banned from undertaking surgical procedures following concerns of mismanagement.
The Victorian Civil and Administrative Tribunal overturned her suspension last week.
The ban on the clinic is still in place.
It had come under scrutiny following the death of 30-year-old mother Harjit Kaur, who died in January at the Hampton Park Women's Clinic after what was described as a "minor procedure".
It was later identified as a pregnancy termination.
Dr Kenney was not involved in the procedure and did not provide clinical care to Ms Kaur.
A coronial investigation into Ms Kaur's death is under way and autopsy results showed no evidence of complications after surgery and ruled out adverse effects of anaesthesia, infection and other conditions or reactions.
The tribunal last week ruled Dr Kenney can continue to treat patients, until the matter is heard before a full tribunal, as long as she doesn't hold a governance role.
Tribunal member Elisabeth Wentworth said submissions from the health department raised concerns about Dr Kenney's capacity as medical director and proprietor of the clinic.
The Medical Board of Australia said Dr Kenny was responsible for the failures identified by the department and put patients at serious risk, as well as employees.
The board said her inability to manage those failures reflected her capacity to practise medicine generally and "put all her patients at risk".
In her written findings, Ms Wentworth disagreed with the sentiments and said those risked were mitigated by the ban on the clinic.
She said continuing Dr Kenney's ban would be "potentially disastrous" for her as well as the future of the clinic that provides reproductive health care to women in Melbourne.
"While the safety of the public must necessarily be the prime concern, it remains the case that public safety should be secured with as little damage to the practitioner as is consistent with its maintenance," Ms Wentworth said.
Hampton Park Women's Health Clinic is a private clinic that opened in 2008 and provides pregnancy terminations, vasectomies, contraception, cervical screening and iron infusions.
The clinic's website on Tuesday said surgical terminations, sleep vasectomies and IUD with anaesthetic were no longer available.
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