Mr Justice Treacy issued an order to scrap the disputed findings after being told the current watchdog, Dr Michael Maguire, consented to the move.
His ruling represents a victory for the victims' families, and paves the way for a new investigation into the shootings.
The six men who died, all Catholics, were killed when UVF gunmen went into the Height's Bar in rural Co Down in June 1994.
The killers opened fire indiscriminately as customers watched the Republic of Ireland play Italy in a World Cup football match.
Those shot dead included 87-year-old Barney Green, one of the oldest victims of the Troubles.
Also killed were Adrian Rogan, 34, Malcolm Jenkinson, 53, Daniel McCreanor, 59, Patrick O'Hare, 35, and Eamon Byrne, 39.
Five others were seriously wounded.
No one has been convicted of the murders, although 16 people have been arrested in connection with the attack.
Victims relatives suspect the RUC investigation was undermined in order to protect informants.
In June last year former Police Ombudsman Al Hutchinson found there was insufficient evidence of collusion between police and the loyalist gang.
He did identify failings in the investigation, criticising it for a lack of diligence, focus and leadership.
His report was branded a whitewash by the victims' families, who launched judicial review proceedings in a bid to have it overturned.
In court on Thursday, it was confirmed that Mr Hutchinson's successor, Dr Maguire, has now agreed to the relief sought.
David Scoffield QC, appearing for Dr Maguire, said: "The Ombudsman is not simply overturning his predecessor's statement.
"Rather, he is consenting to the court quashing that statement on limited grounds."
Mr Justice Treacy then confirmed he would make the order requested and awarded costs to the Loughinisland families.
He added: "Of course, everybody has acknowledged that the present Ombudsman has behaved very properly and promptly in addressing the matter in the way he has.
"The order for costs is no reflection on him."
Lawyers for the families described the outcome as a significant milestone in their campaign to establish the truth surrounding the atrocity.
Niall Murphy, of Kevin R Winters, said it was the first successful judicial review of a report by the Police Ombudsman's Office.
"Our clients strong criticisms, made immediately in the wake of the publication of the report in 2011, have been vindicated and they deserve credit for their perseverance and dedication to establishing the truth about what happened to their loved ones," he said.
"The decision also provides for a brand new re-investigation."
Emma Rogan, whose father Adrian was among those killed in the shootings, said the outcome vindicated the families' belief that the original report was flawed and irrational.
She added: "It is a disgrace that the onus was put on us to take the Office of the Police Ombudsman to the High Court to drag the truth out of the facts that only his office are aware of.
"The conclusion of Al Hutchinson's flawed report was that the complaint of collusion was ruled out due to insufficient evidence.
"The reason that there is insufficient evidence is that the RUC kept destroying the evidence."