Victoria Police said 150 people gathered at Caulfield Shule on Monday evening after a planned pro-Palestine protest was called off at the 11th hour due safety concerns.
A 39-year-old Brunswick East man is expected to be charged with breaching the peace and failing to move on.
He was bailed to appear at Moorabbin Magistrates Court on March 14.
"This peaceful demonstration has been cancelled due to the threats made by Zionists against protesters," pro-Palestine organisers posted on social media.
Police encircled a small group of pro-Palestine activists who turned up at the rally. (Diego Fedele/AAP PHOTOS)
Despite the cancellation, there was a visible police presence near the synagogue in Caulfield North, in Melbourne's southeast, where a sea of Israeli flags far outnumbered those for Palestine.
Specialist police encircled a small group of pro-Palestine supporters, who held anti-Zionist signs saying "nothing is more anti-Semitic than Zionism", in an attempt to keep them from the larger pro-Israel group.
The planned demonstration was in response to a talk organised by the Australia/Israel and Jewish Affairs Council that included former Israeli justice minister Ayelet Shaked, whose visa into Australia was reportedly rejected.
It comes before school students calling for a free Palestine are expected to hold a demonstration outside Victoria's State Library on Tuesday afternoon.
The latest round of protests follow Victoria's premier condemning a planned pro-Palestine protest targeting Myer's Christmas windows earlier in November.
Premier Jacinta Allan labelled the small group of activists as "morons" before they walked back plans to interrupt the retailer's famed festive display unveiling event.
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