Justice Sally Brown has comprehensively ruled against the father, who can be known only as Peter, denying him any contact with his son, 15, and daughter, 10, after a five-year court battle, waged mostly in their home state of Tasmania.
After spending $100,000 winning court orders in 2006 for access, then trying unsuccessfully to enforce them, Peter could only afford to represent himself in the most recent retrial.
The Exclusive Brethren paid for the mother, Elspeth, to hire one of Melbourne's top family court QCs, Noel Ackman, as well as a junior barrister and a solicitor.
The church's "doctrine of separation" prevents people who have left the fold having any relationship with those still inside, including their own children.
Early in 2007, Justice Robert Benjamin sentenced the mother and two male relatives to four-month suspended jail sentences for failing to encourage the children to go with their father. These sentences were overturned on appeal.
Justice Brown's judgment, delivered in Melbourne on Thursday, ruled for the Brethren mother because during the course of the case the children's relationship with the father had broken down, and there was no prospect of re-establishing it.
The judge blamed the father for this, saying that his attempts to make sure that earlier court orders were obeyed had alienated the children from him and that parts of his application were "cruel and punitive" towards the children.
The mother fell ill with a recurrence of breast cancer after Justice Benjamin's ruling in 2007, and the "family narrative" blamed the father for this.
"It is clear that the mother attributes responsibility for the recurrence of her cancer, at least in part, to the trauma she experienced when sentenced," Justice Brown said. Whether or not this was true was "less relevant than its currency in the home".
The daughter had "taken on board" this message and had torn up and returned a card her father had sent her, saying if he wanted her to be happy "he should just leave us alone".
However, she rejected the father's suggestion that the Exclusive Brethren had prompted this behaviour, despite evidence over many years that the sect encourages young children to reject their lapsed parents.
In 2006, a court-appointed psychologist described the Brethren's attempts to turn the children against Peter as "psychologically cruel, unacceptable and abusive" to the children and at "the highest end of psychological abuse".
But Justice Brown's views on the Brethren were generally positive: their religious conviction was as "vital to them as the air they breathe", and "they perceive a life lived outside their faith as unsustainable". She questioned whether it was their policy to remove children from non-Brethren parents, quoting a report to her that said that "the church says in its publication this is not the case".
Justice Brown said it was false to think, as the father did, that this case was "a duel between law and religion".
The father said the few times he had had contact, the children had "warmed up" to him, but the opinion of a court-appointed consultant, Ineke Stierman, was that the daughter's "youth and courtesy explain her relatively polite responses". As for the son, one visit had ended with him curled in a foetal position in the cubby house and refusing to eat.
Having "nothing to do with them now might show ultimate caring", Ms Stierman recommended.
Justice Brown accepted that the result of her judgment was that "the children will not spend time with anyone who speaks positively about the father".
The father had applied for custody of both children but late in the case changed his position, asking for custody of his daughter and access to his son. The judge condemned this as "indicative of a significant lack of understanding of the children's needs" .
The mother's application was to have custody of the children until she died, following which they be cared for by an older sister and her husband.
Although Justice Brown did not rule on what would happen after the mother's death, she agreed the children needed support by their extended family "during these traumatic years", that the girl had bonded with her older sister, and that this must take priority over any relationship with the father, or "any questions about the Exclusive Brethren's compliance with court orders".
Although Ms Stierman suggested contact of "an hour or two, once or twice a year", Justice Brown said she could see no benefit to that. Instead, Peter could, at his expense, be provided with a copy of their school reports, photos and newsletters as long he obtained them at a time when any family members "are not likely to be on the school premises".
Asked by The Sunday Age if he had a message for his children, Peter, who himself grew up without a father because of the Brethren's doctrine of separation, said: "I just want them to know I tried my best."
The Exclusive Brethren declined to comment, saying it was a private family matter.