Pell, 77, will be eligible for parole in three years and six months and, if released, will be required to register as a sex offender for life.
Sentencing Pell on Wednesday, Victorian County Court Judge Peter Kidd labelled the cardinal's moral culpability as high as he outlined his two attacks on the boys over a month apart.
The offences against two 13-year-old boys took place after Sunday mass in late 1996 and early 1997 in a room and a corridor at St Patrick's Cathedral, in Melbourne, where Pell was archbishop.
Pell went on trial for the offences in December previous year and a jury returned unanimous guilty verdicts.
Reporting of the trial and verdict was suppressed by the court to avoid prejudicing a second trial, which crown prosecutors abandoned in February after the judge ruled some prosecution evidence couldn't be submitted.
Pell maintained his innocence throughout and has filed an appeal, which is set to be heard in June.
Asked by a reporter outside court after the sentencing whether the case against Pell amounted to a witch hunt, his lawyer Robert Richter gave a rueful smile.
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. Everything is overshadowed by the forthcoming appeal".
Pell must serve a minimum of three years and eight months, but not everyone is convinced justice has been done.
The Royal Commission found that seven percent of Australian priests had been accused of sexual abuse between 1950 and 2011, the average age of their victims was 11 for girls and 12 for boys.
Chief Judge Kidd during the sentencing hearing.
The broadcast will only show the judge, and not the courtroom, which is expected to be packed with advocates of abuse victims, Pell's supporters and the media.
Sometime later, the complainant said he was again attacked by Pell who pushed him against a wall, fondled his genitals and then walked away.
One of the victims has since died of a drug overdose in 2014.
Worshipper Darryl D'Souza said Pell's conviction and sentencing was a sad situation for Catholics, but it did not change his belief in God or the church.
His conviction has rocked the Catholic Church, where he had been one of the Pope's closest advisers.
The sentence "makes a mockery of the concept of true accountability and is not a sentence commensurate with the crimes committed and the harm reaped", Blue Knot Foundation president Cathy Kezelman said in a statement.
In the decades since, evidence of widespread abuse has emerged globally.
The cardinal's crimes have drawn widespread condemnation, though he has retained the support of some high-profile figures in Australia.
"You are not to be made a scapegoat of the failings or perceived failings of the Catholic Church", said Kidd, criticizing a "lynch mob mentality" among the public.
The Melbourne court allowed the live broadcast of Kidd reading out his sentencing remarks in a commitment to the principles of "open justice".