In a 2003 letter obtained by the Australian Broadcasting Corporation, Pell told Jones that an internal report did not support his accusation of attempted aggravated sexual assault by Father Terence Goodall.
It had in fact accepted all of Jones's allegations.
Pell said earlier this week that the letter to Jones was "badly worded and a mistake" but denied it was part of a cover-up and on Friday ordered an independent, church-appointed panel to investigate the claims.
'Scores' of clergy prosecuted
Benedict's visit to Australia comes just three months after trips to Washington and New York during which he apologised for the paedophile priest scandals that have rocked the Catholic church in the United States.
"It must be clear being a priest is incompatible with this behaviour because priests are in the service of our Lord," Benedict said on Saturday.
"We have to reflect on what was insufficient and our education and our teaching [of priests]. This is the essential content of what we will say [as we] apologise."
Broken Rites Australia, which helps victims of church-related sexual abuse, has urged Benedict to "offer a proper apology personally to a group of victims of church sexual abuse".
The group says more than 50 Australian priests and brothers have been prosecuted for sexual crimes.
Benedict is in Australia to preside over World Youth Day, during which he will highlight the threat of climate change.
The 81-year-old pope will spend three days resting at a retreat in Sydney before taking part in the festival.