His parents told the newspaper he was mocked about his circumcised penis so badly that he wet himself instead of using the toilet.
The boys — who attended Cheltenham Secondary College and Hawthorn West Primary school respectively — have moved schools, according to The Age.
The five-year-old's mother told the newspaper language used against her child by the bullies mirrored the anti-Semitic language of the Holocaust.
"I grew up with Holocaust survivors. I used to go to synagogue with my uncle, who was a Holocaust survivor, and those were the words, literally, he was taunted with when he was five," she said.
The shocking incidents have stoked fears that anti-Semitic bullying in Australian schools is on the rise — with a Jewish leader telling news.com.au Australia is facing a "crisis of huge proportions".
Anti-Defamation Commission chair Dvir Abramovich said the incidents were "only the tip of the iceberg" and there was an "exodus of young Jewish people out of the public school system".
"No child should be singled out and victimised simply because of their faith, and the fact that this is happening on a daily basis is shameful and outrageous," he told news.com.au.
"To think that in 2019 Jewish pupils are subjected to violence, verbal insults and taunts, bigoted jokes, social exclusion, demeaning text messages and malicious Facebook posts is heartbreaking.
"Not surprisingly, there is mounting evidence that families are forced to take their children out and to enrol them in Jewish-day schools due to a growing sense of insecurity and fear that their kids will be harmed simply because of who they are. The kids are shaken and traumatised."
A Department of Education spokesperson said anti-Semitism was taken "very seriously" and "has no place in our community or our schools".
"All students have the right to feel safe and supported by their school," the spokesperson said.
"We put in place supports for all students who are affected in incidents of aggression and violence in schools."
It is understood Cheltenham Secondary College undertook disciplinary action against the boys involved, while the incidents at Hawthorn West Primary school have been investigated by staff.
James Merlino Victoria's Deputy Premier and Minister for Education said the incidents are "appalling".
"I am still very concerned by the parents' reports and I have asked for an immediate review into how both schools have handled these matters, to ensure they were dealt with appropriately," he said.
News.com.au has contacted both schools for comment.