The Victorian government's inquiry into the handling of child abuse by religious and other organisations has been told Cardinal Pell was present when the grade three student at a Ballarat school in the 1960s described to another priest what happened to him.
Cardinal Pell may be asked about the incident after indicating in August he will attend the inquiry if asked.
The Archdiocese of Sydney's communications office spokeswoman said it cannot comment while an inquiry is under way.
The victim, a student at St Alipius school in Ballarat, was raped by principal and teacher Christian Brother Robert Charles Best in 1969.
Best was last year convicted of 27 offences against 11 schoolboys including two rapes, and jailed for 14 years and nine months.
His victims were from St Alipius, where he was principal, and two
schools he later taught at, St Leo's in Box Hill and St Joseph's in
Geelong.
Two other Christian Brother teachers and the school chaplain from the school were also convicted of child sex offences years later.
Police are now investigating 50 suicides by graduates of St Alipius, all thought to be linked to sex offences by Brother Best and Father Gerald Ridsdale who operated the parish.
Solicitor Dr Vivian Waller, who has represented hundreds of sexual assault victims alleging abuse by religious clergy, outlined the details involving Cardinal Pell in her submission to the inquiry.
Dr Waller says Dr Best's victim returned to class after the rape and told his teacher Christian Brother Fitzgerald, now deceased, who forcibly and repeatedly struck him until he retracted what he said.
The victim then went to the St Alipius presbytery and asked to speak to George Pell.
"I am instructed that George Pell refused to speak with him, but that George Pell was present when (the victim) described to another priest what had happened to him," Dr Waller wrote in her submission.
Dr Waller said the victim's case, together with the criminal convictions of Brother Best and teachers at the school Brother Edward Dowlan and Brother Stephen Farrell, should have led to a thorough investigation of a possible pedophile ring operating within the ranks of the Christian Brothers.
She said the church should have been proactive in looking into the matters and tracking down other students who may have been victims.
"It cannot be said that the Christian Brothers and the church more broadly were not on notice of significant and disturbing allegations," she said. "As far as I can ascertain, the Christian Brothers did not refer matters to the police, nor did they conduct an internal investigation."
Dr Waller, who is representing 50 men who allege they were physically or sexually abused by various Christian brothers and a further 25 clients who allege they were abused by other Catholic clergy, wants a royal commission into Catholic clergy abuse.
The Catholic Church in Victoria has backed mandatory reporting of child abuse to police for religious ministers and personnel, with an exemption for information received during confession.
Catholic Archbishop of Melbourne Denis Hart said a balance needed to be struck between the community's responsibility to prosecute criminal conduct and the victim's rights to privacy.