Prosecutor Fran Dalziel told the court on Tuesday that the Ballarat charges had been dropped and asked for the suppression order to be lifted.
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The victim who testified at Pell's trial said after the conviction was revealed that he has experienced "shame, loneliness, depression and struggle." In his statement, the man said it had taken him years to understand the impact the assault had on his life.
Lawyer Lisa Flynn said the father of the second victim, who died of a heroin overdose in 2014 at the age of 31, is planning to sue the church or Pell individually once the appeal is resolved.
Pell's lawyer, Robert Richter, initially wanted details of the trial suppressed until his appeal was heard, but later withdraw the application.
Pell was surrounded by a crush of cameras and members of the public as he was ushered from the courthouse to a waiting car. "You're a monster!" one man shouted. "You're going to burn in hell, you freak!"
"Are you sorry?" one woman shouted. Pell did not respond.
Another of Pell's lawyers, Paul Galbally, said Pell continued to maintain his innocence.
The revelations came in the same month that the Vatican announced Francis approved the expulsion from the priesthood of a former high-ranking American cardinal, Theodore McCarrick, for sexual abuse of minors and adults.
The convictions were also confirmed days after Francis concluded his extraordinary summit of Catholic leaders summoned to Rome for a tutorial on preventing clergy sexual abuse and protecting children from predator priests.
The jury convicted Pell of abusing two boys whom he had caught swigging sacramental wine in a rear room of Melbourne's St. Patrick's Cathedral in late 1996, as hundreds of worshippers were streaming out of Sunday services.
Pell, now 77 but 55 at the time, had just been named the most senior Catholic in Australia's second-largest city, Melbourne.
The boys were both 13 years old. The jury also found Pell guilty of indecently assaulting one of the boys in a corridor more than a month later.
Pell had maintained his innocence throughout, describing the accusations as "vile and disgusting conduct" that went against everything he believed in.
Richter, his lawyer, had told the jury that only a "mad man" would take the risk of abusing boys in such a public place. He said it was "laughable" that Pell would have been able to expose his penis and force the victim to take it in his mouth, given the cumbersome robes he was wearing.
Both he and Chief Judge Peter Kidd urged the jury of eight men and four women not to punish Pell for all the failings of the Catholic Church, which in Australia have been staggering.
"You must not scapegoat Cardinal Pell," Kidd told the jury.
Along with Ireland and the U.S., Australia has been devastated by the impact of the clerical abuse scandal, with a Royal Commission inquiry finding that 4,444 people reported they had been abused at more than 1,000 Catholic institutions across Australia between 1980 and 2015.
Pell's downfall will invariably tarnish the pope, since Francis appointed Pell economy minister in 2014 even though some of the allegations against him were known at the time.
In October, Francis finally cut Pell loose, removing him as a member of his informal cabinet. Pell technically remains prefect of the Vatican's economy ministry, but his five-year term expires this year and is not expected to be renewed.