The sentence brings to a close the decades-long fight by sisters Dassi Erlich and Elly Sapper for justice after their abuse at the hands of the respected mentor and mother-of-eight.
Leifer cried as her sentence was handed down.
She was convicted by a jury earlier this year of 18 charges of sexual abuse, including rape and indecent assault.
She was acquitted of nine other charges, including five against the siblings' older sister Nicole Meyer.
All three sisters were in the Victorian County Court on Thursday when Judge Mark Gamble handed down his sentence and ordered Leifer serve at least 11.5 years in prison.
Leifer was not there in person, and instead watched proceedings by videolink from the Dame Phyllis Frost Centre, Melbourne's maximum security prison.
Leifer targeted the sisters between 2004 and 2007 when they were students at the Adass Israel School, and later in their first year a student teachers.
She was aged between 37 and 41 at the time.
Ms Erlich was aged between 16 and 19 and Ms Sapper aged 17 and 18.
In handing down the sentence, Judge Mark Gamble formally took into account 1129 days Leifer spent in custody in Israel, during extradition proceedings, and 940 days in custody in Australia.
He also applied a modest reduction in the sentence, taking into account 608 days under house arrest.
Those days were punitive, he said, but he also took into account accusations she had exaggerated and intensified her mental health conditions to frustrate extradition proceedings during that time.
In an hours-long sentencing hearing, Judge Gamble detailed the grooming and abuse inflicted upon the sisters, who had a difficult home life.
Leifer arrived from Israel in 2001 as menaheles at the Adass Israel School - a highly revered principal position giving her responsibility for the school's ethos and religious teachings.
The sisters viewed Leifer as a mentor and welcomed the alone time she arranged with them, during which she professed to love them like a mother.
But Judge Gamble said that grooming allowed Leifer to facilitate the abuse.
She also threatened to expose their home life.
"She knew a lot of things about me and implied if I said anything she would share those things about my home life, which was a big shame to me at the time," he read from Ms Erlich's evidence.
Judge Gamble said some offending against Ms Sapper may have appeared brazen, but she had already tested the waters and as Ms Sapper did not complain she may well have felt confident in continuing to act as she did.
Ms Erlich's statement in court about the impact of Leifer's abuse was a powerful illustration of the legacy the insidious abuse left her with, he said, noting one of the most egregious aspects of the harm was the effect it had on her as a mother.
Ms Sapper described dealing guilt, shame and fear, and continues to blame herself for allowing Leifer to love her.
But Judge Gamble said the sisters were commendably resilient and surprisingly optimistic.
"They were completely innocent victims of the predatory behaviour of Mrs Leifer, and it is she and she alone who should feel guilty," the judge said.
Leifer was educated in Israel and had an early passion for teaching, Judge Gamble said.
Her former colleague, Malky Fixler, said she had been a much respected person within the Adass Israel Community, but the judge said her character and good reputation assisted her in committing the offences.
He noted prison had been difficult given she is the only Jewish woman there, English is not her first language and she has only been able to have two personal visits from immediate family, who all live overseas.
The hearing room was full for the sentence, with former premier Ted Baillieu and Victorian MP David Southwick in attendance.
A psychologist said Leifer was struggling with the jury's guilty verdicts, maintaining she is not guilty.
The judge came to the view Leifer's experience in custody in Australia had been onerous and that would likely continue.
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