Theodoros Tsalkos was found guilty of kidnapping, rape and gross indecency by a jury and in 2023 he was sentenced to up to 13 years and six months in jail.
He was aged 25 in 1987 when he was accused of pretending to be an undercover police officer to pick up two sex workers, who were aged 15 and 16, in St Kilda.
It took more than three decades for Tsalkos to face trial, in 2022, where he was accused of holding the girls captive in his car and raping them over several hours.
County Court Judge Rosemary Carlin told Tsalkos "what you did was pure evil", and labelled the alleged crimes as "sadistic and vile" as she handed him an eight-year and two-month minimum jail term.
Tsalkos, now aged in his 60s, appealed against his convictions on several grounds, including that a miscarriage of justice occurred during the jury's directions.
He claimed the jury was not warned that a mother's evidence of one of the victim's distress carried little weight, when jurors were invited to use it as "independent" evidence in their decision.
The Court of Appeal on Thursday, by a majority, found the judge had misdirected the jury and set aside his convictions, ordering a new trial
"We have concluded a substantial miscarriage of justice occurred," Justices Karin Emerton, Stephen McLeish and Christopher Boyce said.
"We would grant leave to appeal against conviction; allow the appeal; set aside the applicant's convictions; and order a new trial."
In a separate decision, Justice Phillip Priest disagreed with his fellow judges on a second appeal ground and found it should also succeed.
This ground concerned failings by defence and prosecutors during the jury trial around credibility and issues in the prosecution's closing address.
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