The judge has begun his remarks by acknowleding that Pell was "one of the most senior figures within the Catholic Church globally" and a "publicly vilified figure" among some sections of the community.
Some described the prosecution as proof the church is no longer above the law, while others suspect Cardinal George Pell has been made a scapegoat for the church's sins.
Pell, who has been in custody since that time, is the most senior Catholic clergyman to be convicted worldwide for child sex offences and was until he took leave in 2016 to fight the case the third-most powerful man in the Vatican and as a Cardinal, Australia's most senior Catholic.
"In my view, your conduct was permeated by staggering arrogance", said Justice Kidd in handing down the sentence after Cardinal Pell was convicted of five counts of sexually abusing two children.
Pell, 77, maintains his innocence and intends to challenge the conviction in the Court of Appeal, which will be heard in June.
"To other victims of clerical or institutional sexual abuse, who may be present in court today or watching or listening elsewhere, this sentence is not and can not be a vindication of your trauma", Kidd said. "Both victims were visibly and audibly distressed during this offending", he told Pell.
"There was a clear relationship of trust with the victims, and you breached that trust and abused your position", Kidd said.
The other boy died in 2014. He will be eligible for parole after three years.
"I am conscious that the term of imprisonment which I am about to impose upon you carries with it a real, as distinct from theoretical, possibility that you may not live to be released from prison".
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The cardinal faced a maximum 50 years in prison for the five charges.
In a rare move reflecting interest in the high-profile case, the sentencing will be broadcast live on television although the camera will only show the judge and not the court room.
During his trial, Pell's own lawyer described the burly 1.9 meters (6 foot and 3 inches) tall cardinal as the "Darth Vader" of the Catholic Church.
Earlier campaigner against child sexual abuse, Leonie Sheedy, expressed her hope for justice.
After mass one Sunday in the late 1990s, Judge Kidd recounted, Pell caught two choirboys drinking communion wine in the priest's sacristy and one by one forced them to engage in sex acts, despite their sobs and pleas for him to let them go.
Pell sat emotionless and unflinching as the sentence was handed out.
The sentence has been criticised by some survivors of child sexual abuse and their advocates, who claim the punishment is not commensurate with the crime. He ruled 12 months of the first sentence of two years and six months could be served concurrently with the base sentence, along with four months of the second sentence of two years and six months.
Normal procedure will now see Pell transferred back to the Metropolitan Assessment Prison in West Melbourne, where the former Vatican treasurer has spent the last two weeks awaiting sentence.