Pell went on trial for the offences in December a year ago and a jury returned unanimous guilty verdicts. A court order had suppressed media reporting the news until last month.
Pell, 77, was convicted late last year by a Melbourne court on one charge of sexual penetration of a child under 16 years of age and four charges of committing an indecent act on children.
Judge Kidd rejected a prosecution argument that Pell continues to pose a limited risk of re-offending because he shows no remorse or insight into the offending, given he maintains his innocence.
Kidd made clear that Pell was not being made a "scapegoat" for the Catholic Church's failings and that he was being sentenced only for the crimes convicted by the jury.
Judge Kidd addressed the current climate of anger with the Catholic Church at Pell's February hearing when he said, "The Catholic Church is not on trial and I'm not imposing a sentence on the Catholic Church".
The surviving victim said everything was overshadowed by Pell's upcoming appeal.
Under the terms of the sentencing, Pell must serve a minimum of 3 years and 8 months before he is eligible for parole.
The boys had "nicked off" from the rest of the choral procession and were taking swigs of sacramental wine before the cardinal found them, opened his robe, exposed his penis and sexually assaulted them.
"Facing jail at your age in these circumstances must be an terrible state of affairs for you", Kidd said, the Guardian reported.
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The depiction of Pell as a man wronged has infuriated survivors of church sex abuse who say that casting victims as liars and priests as beyond reproach perpetuates a culture that allowed abuse to thrive within the Catholic Church for decades.
According to the BBC, Pell plans to appeal the convictions.
Sometime later, the complainant said he was again attacked by Pell who pushed him against a wall, fondled his genitals and then walked away.
The most senior Catholic of all, Pope Francis, who faces calls to strip Pell of his Cardinal status, has said he would withhold comment until the appeal process was concluded. The second victim - who died of a heroin overdose in 2014 - also must have suffered "an immediate and lasting impact" and his father's statement was considered.
"In sentencing you today, I am not sentencing the Catholic Church ... it is George Pell to be sentenced".
If defrocked, Pell would be the highest profile figure to be dismissed from the priesthood in modern times and only the second Roman Catholic prelate to lose the title of cardinal in almost 100 years.
While awaiting sentencing, prisoners, for the most part, keep their civilian clothes, but now Pell's belongings will be taken and he will be given a green prison tracksuit for the first time.
Only the judge was made visible to viewers in the TV broadcast, which was cut immediately after the sentence was delivered.
"I don't think six years is long enough", said a victims' advocate outside the court who gave her name as Rhonda.