Chief Judge Peter Kidd told the Melbourne court that the sentencing reflected the crimes committed and were not directed against the Catholic Church.
In emotional scenes, those abused by others joined together in Melbourne to witness the outcome of the sentence hearing.
The cardinal, a household name in Australia with friends that include prime ministers and business magnates, maintains his innocence and will appeal.
Pell was found guilty by a jury last December of sexually abusing the choirboys after a Sunday mass in December 1996 and then assaulting one of them a second time two months later.
The other boy died in 2014.
"It is hard for me to allow myself to feel the gravity of this moment" the victim, who has not been identified, said though his lawer Vivian Waller. Pell signed documents that registered him for life as a serious sexual offender before he was led from the dock by four prison officers.
He faced a maximum sentence of 50 years in jail.
He says he must technically have regard of "protection of the community from you", however he believes Pell does not pose this risk.
"None of it seems to fit the crime", she said.
"You were confident your victims would not complain".
His conviction has rocked the Catholic Church, where he had been one of the Pope's closest advisers.
"I conclude that your decision to offend was a reasoned, albeit perverted one", Kidd said.
Crowd gathers to watch the live stream of Cardinal George Pell's sentencing.
Pell sat emotionless and unflinching as the sentence was handed out. "Everything is overshadowed by the forthcoming appeal".
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In considering the sentence, Kidd said he had taken into account Pell's advanced age, health problems and the fact that he had lived "an otherwise blameless life in the 22 years since the offending".
In the decades since, evidence of widespread abuse has emerged globally.
Pell's fate within the church has yet to be decided.
The Vatican has said that it will...
Several of Pell's other high-profile friends in Australia have leaped to his defense, questioning the jury's verdict and predicting the cardinal would be exonerated on appeal.
"As I directed the jury who convicted you in this trial, you are not to be made a scapegoat for any failings or perceived failings of the Catholic Church".
"In my view, the first episode in the priest's sacristy involved a brazen and forceful sexual attack on the two victims", Kidd said.
"The acts were sexually graphic. Both victims were visibly and audibly distressed during this offending", he said, adding Cardinal Pell's behaviour had a "nasty element" to it.
The BBC reports that Pell can apply for parole after three years and eight months.
Pell did not take the stand in his defence, but in a video of his police interview in Rome in 2016 he called the allegations against him "deranged falsehood" and "a load of absolute and disgraceful rubbish".
"Despite this, you still indecently acted against (the boy), and did so with what I consider to be a degree of physical aggression and venom", Judge Kidd said.
Only the judge was made visible to viewers in the TV broadcast, which was cut immediately after the sentence was delivered.
Courts must send an unequivocal message to would-be child sexual offenders, the judge said.
A court order had prohibited media from reporting on the verdict until two weeks ago, when prosecutors abandoned a second trial on charges that Pell had groped two boys in a public swimming pool in the 1970s.