Police were called to Sydney's Chabad Double Bay after reports a man inside a car was pointing what looked like a gun towards congregants in front of the building on Saturday.
Officers followed the car to Kings Cross where they arrested two men and searched their car, allegedly finding an imitation firearm.
Executive Council of Australian Jewry co-chief executive Alex Ryvchin said the alleged incident was disturbing coming just months after a shooting massacre that targeted the Jewish community.
"Threatening and terrifying Jews for laughs. Well done to the police for their swift action," Mr Ryvchin said.
A 22-year-old was charged with using an offensive weapon with intent to commit an indictable offence, possessing an unauthorised pistol and stalking.
A 25-year-old man was charged with possession of an unauthorised pistol.
The pair were refused bail to appear in court on Sunday.
Chabad Double Bay is part of the same broader organisation as Chabad Bondi, which put on the Hannukah event that was targeted by the gunmen in the Bondi Massacre in December.
During that violent attack, 15 people were allegedly killed by Sajid Akram and his son Naveed Akram.
Sajid was shot dead by police and his son is facing 79 charges relating to the December 14 incident, including murder and one count of committing a terrorist act.
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