He was convicted on 11 charges including rape and indecent assault.
A victim said he should have "got life".
62 year old Pidoto was found guilty of the 11 charges in July. They include rape, indecent assault and buggery.
He had denied all the charges.
Judge Ross Howie said Pidoto had abused his position of trust and influence. He said the priest's actions were "a shocking betrayal" of his vocation.
Outside court, Pidoto's last victim said he "should have got life".
"But he's behind bars for a minimum of five years so, for those five years, he can't hurt any more children."
Pidoto was ordained in 1971 aged 26. He sex acts began a year later when he took a 14-year-old boy to the Corpus Christi seminary in Melbourne's east.
Pidoto wore headphones and appeared nonchalant as Judge Howie ordered him to serve at least five years before being eligible for parole. He said "Thank you, Your Honour" after he was sentenced.
Victims angry at sex priest jail term
All good undone by abuse, judge tells priest (CathNews, 11/9/07)