Ex-Brighton Secondary College students Joel and Matt Kaplan, Liam Arnold-Levy, Guy Cohen and Zack Snelling took the state, the school, two teachers and principal Richard Minack to the Federal Court for a months-long trial last year.
Each of them left Brighton Secondary College prematurely and four out of five departed the school because of anti-Semitic bullying.
Chief Justice Debra Mortimer in September found Jewish students were not protected from bullying, discrimination and negligence when they attended the school between 2015 and 2020.
Bullying victim Joel Kaplan rejected an apology from the education department.
She said Mr Minack, as principal, failed to take action to address "a high level of anti-Semitic bullying and harassment of Jewish students" and swastika graffiti at the school.
The chief justice ordered the state to pay the five men more than $500,000 compensation, including interest and legal costs.
She ordered a senior official from the Department of Education to issue a verbal, in-person apology to the five students.
Deputy secretary David Howes made the apology on Tuesday, telling the men the department was being more proactive to claims of bullying and harassment in schools.
"This apology is both an apology directed to the boys for what they suffered and to their families for what they suffered, but it is also an apology to you, the broader Jewish community," he told the Caulfield Hebrew Congregation.
But Joel and Matt Kaplan both rejected the apology, describing it as a sham.
"We asked for an apology for three and a half years and the state refused to do so," Matt Kaplan said to loud applause from the congregation.
"It was, even after winning such a huge court case, an extremely difficult and painful process."
He criticised the decision to send Dr Howes to make the apology rather than a senior government minister or education department official.
"Instead, the apology was given by someone I've never even heard of before," he said.
The men were told Mr Minack was still employed by the education department, which Matt Kaplan described as disgraceful.
They claimed anti-semitism was still happening at Brighton Secondary College, years after they left the school.
AAP has approached the education department for comment.
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