More than a thousand community members were expected to meet at an undisclosed location in Ripponlea to "stand against hate" on Sunday.
The rally will finish with flowers being laid at the synagogue.
"This rally is a moment to unite, reflect and reaffirm our shared commitment to resilience and togetherness in our community," organisers J-United said.
Community members have begun laying flowers outside the Synagogue. (Diego Fedele/AAP PHOTOS)
Cabinet minister Murray Watt described Friday's attack as an "absolutely horrific anti-Semitic attack" before alleging Opposition Leader Peter Dutton had politicised the incident.
Mr Watt also refuted Mr Dutton's claims that the government had made Australia less safe for Jewish people and that Prime Minister Anthony Albanese had not done enough to address anti-Semitism.
The political debate was largely ignited by Israeli Prime Minister Benjamin Netanyahu, who on Saturday condemned the synagogue attack and linked it to Australia's decision to support a non-binding UN General Assembly resolution.
Australia is one of 157 countries, including the UK, Canada and New Zealand urging Israel to end its presence in Palestine.
The Australian Palestine Advocacy Network says any attack on a place of worship is an unacceptable act of hate but has accused Mr Netanyahu of deliberately sow division.
The fire-damaged Adass Isreal Synagogue remains closed to the public. (Con Chronis/AAP PHOTOS)
Although not part of the Adass Israel congregation, Caulfield resident Hallely Kimchi said it was time for more to be done to protect Jewish people.
"It is not about Israel. It's about Jews in Melbourne - forget about Israel at the moment," she said as the rally was getting under way.
"There are people that have been abused and have never been to Israel.
"Jews living in Melbourne should feel safe and proud to do whatever they want and to work without being doxxed or boycotted."
The synagogue remains closed to the public after it was set alight by two masked men in what police have described as a targeted attack.Two of its three buildings were gutted and two congregants who were inside at the time preparing for morning prayers were evacuated, one suffering minor injuries.
Police have confirmed they are also investigating reports of a bullet found on a footpath near the Synagogue in Glen Eira Road on Saturday afternoon.
Community members laid flowers outside a makeshift memorial outside the Synagogue on Sunday morning.
The attack on a place of worship, which was built by Holocaust survivors, has led to a heightened sense of fear in the community, Executive Council of Australian Jewry president Daniel Aghion said.
Victorian Premier Jacinta Allan confirmed increased police patrols to bolster safety into the coming week and pledged $100,000 towards rebuilding.
Despite condemning the attack, she is not expected to attend Sunday's rally.
The incident has meanwhile prompted NSW to consider new laws to better protect religious freedoms.
Premier Chris Minns said he would consider reforms to laws regulating protests outside religious institutions.
A pro-Palestine rally is also planned outside the State Library of Victoria in Melbourne CBD on Sunday that will end with a march through the CBD.
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