The 36-year-old was found guilty of sexual assault by a jury last year and sentenced to spend at least three years in jail.
He has consistently denied he attacked the woman – who cannot legally be named – in her bedroom, arguing the pair had consensual sex.
Prosecutors are now weighing up whether to drop the charges against him, they said in a statement.
Mr Hayne was one of the most high-profile athletes in Australia’s National Rugby League (NRL) and briefly played American football in the NFL.
His 26-year-old accuser told the New South Wales (NSW) District Court the pair had chatted on social media for two weeks before Mr Hayne stopped at her house in Newcastle – about two hours north of Sydney – after a bachelor party in September 2018.
She said Mr Hayne forced himself on her there, despite her saying “no” and “stop”, leaving her bleeding.
Mr Hayne’s appeal was heard in April by a panel of three judges from the state’s top court.
On Wednesday, two of the three ruled that the trial judge had erred in prohibiting cross-examination of the woman over certain text messages, which Mr Hayne’s legal team argued had implied her consent.
When delivering the verdict, Justice Stephen Rothman said that had amounted to a miscarriage of justice, ordering Mr Hayne’s convictions be quashed.
He was granted bail and will be released from prison.
In a statement, the Office of The Director of Public Prosecutions (DPP) said it would “consider [the] judgement” and any decision about a possible retrial would be made in accordance with its guidelines.
Last year’s trial was the third time Mr Hayne has stood before a jury over the same allegations. His first trial ended in a hung jury, and a guilty verdict in the second trial was overturned on appeal.
He has collectively spent almost two years in jail as the legal saga has unfolded, and his accuser has been forced to give evidence and face lengthy cross-examination multiple times.
In her written reasons, Justice Deborah Sweeney said a fourth trial in her view “would not be in the interests of justice”.
Justice Rothman agreed, saying a trial was “unlikely” to occur before the expiry of Mr Hayne’s non-parole period – and he has already served most of it anyway.
However, both emphasised the future of the case was up to the DPP.
A former captain of the Parramatta Eels, Mr Hayne twice won the NRL’s player of the year award and played 11 Tests for Australia.
At the height of his career in Australia, in 2015 he joined the NFL in the US with the San Francisco 49ers.