The 36-year-old had convictions for two counts of sexual assault without consent overturned by an appeals court earlier in June, after which prosecutors revealed they would not pursue a fourth trial.
On Friday, prosecutors formally withdrew the remaining charges, leaving Hayne to walk from Sydney's Downing Centre court free from the allegations for the first time in years.
"The record will reflect that the Crown has discontinued any and all proceedings against Mr Hayne," Judge Craig Everson told the court.
A jury found Hayne guilty in April 2023 and he was sentenced to a maximum of four years and nine months in prison.
It was alleged he raped a woman with his hands and mouth at her Newcastle home on the night of the 2018 NRL grand final.
But earlier in June the NSW Court of Criminal Appeal quashed Hayne's convictions on the basis a judge erred in not allowing the complainant to be further cross-examined during the trial.
Three separate criminal trials were told the woman, who cannot be identified for legal reasons, changed her mind about having sex with Hayne after realising he had a taxi waiting outside her house.
The ex-NRL player's barrister, Tim Game SC, told an appeal hearing in April that the woman deleted messages between herself and Hayne that demonstrated she had initially shown a sexual interest in him.
His defence team also argued the woman should have been cross-examined on why she allegedly told police, "If those message get out, I'm f***ed and he will get off."
Judge Graham Turnbull, who oversaw Hayne's third trial, refused requests for the woman to be cross-examined on the statement, saying it carried "almost infinitesimal weight".
Hayne's quashed convictions followed a hung jury in his first trial in 2020 and a previous appeal overturning the 2021 guilty verdict from his second trial.
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