Ellis - who spent seven years in prison - always maintained his innocence, taking his case to every level of New Zealand's justice system.
He lodged his last-ditch appeal to the country's highest court in 2019, but died of bladder cancer before any hearing could be held.
In a legal first, the Supreme Court ruled that his appeal could continue despite his death - a departure from common law norms.
Today, in a unanimous verdict, the court's justices found a "substantial miscarriage of justice" had occurred as a result of unbalanced or inadmissible expert evidence given at the original trial in 1993, as well as contaminated evidence from the child complainants.
Ellis was convicted of 16 charges of sexual offending against seven children.
The Supreme Court said the judgement marks the end "of a long and painful journey" for many people involved in the case.
"With the benefit of hindsight, the court considered that the special care and attention required for a case of such unprecedented complexity was underestimated at the time of the investigation and trial and this resulted in a miscarriage of justice."
The court stated that its judgement was not to be read as a criticism of the parents, the complainants or those involved in the investigation and trial.
Alongside its substantive ruling, it also released its reasons for allowing the appeal to go ahead despite Ellis' death.
In the majority, Justices Winkelmann, Glazebrook and Williams said the public interest meant it was in the interests of justice to let it proceed, and the grounds for the appeal were strong and raised systemic issues.
However, Justices O'Regan and Arnold said they would not have exercised the discretion to allow the appeal to continue, saying the the high level of stress and public scrutiny of the appeal for complainants and their whānau outweighed other factors in this case.
They also said they viewed the public interest factors as having less value than attributed to them by the majority judges, especially given the legislative changes that have occurred since Ellis' trial took place.
The fact this verdict was reached was the result of a legal first in this country. The Supreme Court granted Ellis' legal team leave to appeal in 2019, but Ellis died of cancer weeks later.
Normally, a person's legal proceedings die with them, but in reasoning released at the same time as the verdict, the justices said the public interest and weight of a potential miscarriage of justice presented a reason to allow the challenge to proceed despite his death.
This was Ellis' third and final appeal. He unsuccessfully brought his case to the Court of Appeal in 1994 and 1999, and repeated applications to ministers and the Governor General for Royal prerogatives of mercy were also denied.
Two threads - expert evidence and contamination
Key parts of the decision was whether the expert evidence unfairly and improperly bolstered the children's evidence, and whether the jury was properly told about the risk of contaminated evidence.
The contamination rose from direct and suggestive questioning by the children's parents before their interviews with authorities, the ruling said.
There was also the risk of contamination because of other influences on the complainants outside the interview process.
In both previous appeals, in 1994 and 1999, the court found the issues had been properly considered and dealt with at the original trial.
But the Supreme Court concluded the jury was not sufficiently informed of the level of risk from the evidence, and that there had been studies on the issue in the time since the trial.
It said evidence given by specialist psychiatrist Karen Zelas, who gave evidence for the Crown, helped the police investigation and was involved in supervising complainant interviews, lacked balance.
Even on the basis of scientific knowledge in the early 1990s, the court said Dr Zelas' evidence "substantially understated" or mischaracterised the risk of contamination.
Its admission at trial was an "error of law", the Supreme Court said.
Dr Zelas gave evidence on whether a child's behaviour could be consistent or not with that of sexually abused children, including behaviours such as problems with sleeping and bedwetting - but also sexualised behaviour.
"She failed to fairly inform the jury of other possible explanations for the behaviours and discounted/minimised explanations offered by the defence.
"Dr Zelas' multiple roles in relation to the investigation and prosecution may have contributed to that imbalance in her evidence," the court found.
Reasoning for allowing appeal
The fact the Supreme Court allowed the case to proceed despite Ellis' death was something of a precedent-setting measure in itself, drawing attention for its incorporation of tikanga Māori and whether it was relevant in this case.
Alongside its substantive judgement today, the Supreme Court released its reasons and thinking behind its decision to allow Ellis' appeal to proceed.
In 2019, on the suggestion of the justices themselves, Ellis' lawyers argued that tikanga was part of New Zealand's common law.
Under tikanga, the customary rules which govern Māori life, Ellis would have a right to clear his name or re-establish his mana, even if dead. In Māoridom, mana and reputation carries on in whakapapa, rather than an individual's life.
That raised interest in legal circles about the potential wide-ranging precedent such a decision could set.
For years, tikanga Māori has increasingly been recognised by courts and legislation, but the reasonings of the country's highest court was expected to clarify questions about how two systems and world views could be melded.
Even among Māori, there was concern about whether Crown institutions, like courts, should ever be the arbiter of tikanga.
Yet in the decision released today, the justices said the granting of the continued appeal was specifically tied to the circumstances of Peter Ellis, in terms of the public interest, concern and the possibility of a miscarriage of justice.
While considerations of tikanga and Ellis' continued reputation could be incorporated, they said, it stood alongside other factors, such as the interests of finality, the weight of personal and public interest, and whether there was a potential miscarriage of justice to be addressed.
Three of the justices - O'Regan, Glazebrook, and Arnold - wrote that while tikanga may be relevant, it "did not necessitate a modification of the test set out."
The majority of the judges also said the public interest in the case of Peter Ellis meant it was in the interest of justice to allow the appeal to proceed.
"The grounds of appeal are strong and raise systemic issues," they wrote.
Other points raised by Ellis' legal team
The justices' substantive decision made comments on other points argued by Ellis' lawyers.
They said "allegations that could be described as fantastical" which came from interviews with complainants which could have assisted the defence if they were played at trial did not add to the risk of mistrial.
The courts said the fact that the jury was given transcripts of interviews played by the Crown at trial, but not ones for those played by the defence was unsatisfactory but would not have allowed an appeal to go ahead on that basis alone.
It said medical evidence about complaints given at the trial - when assessed against today's standards - was incorrect, and was another reason for concern about the verdict.
