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Dozens of the tennis star's supporters gathered outside the Flinders Lane office in the centre of the city on Monday night.
Videos show a man jumping on a black car after it left the building.
The crowd, some waving Serbian and Greek flags, surrounded police while chanting "Novak", before fans were pepper sprayed by the officers.
Victoria Police said they were forced to use the spray "due to the aggressive behaviour of the crowd".
A 27-year-old Hampton man was arrested during the incident but has since been released from custody.
He is expected to be charged on summons with assaulting police and "acting in a riotous manner".
Two police, a male leading senior constable and a female constable, received minor injuries that did not require medical treatment.
Djokovic had an immigration official's decision to cancel his visa overturned by a Federal Circuit Court judge on Monday, but Immigration Minister Alex Hawke still has discretionary power under the Migration Act to remove him from the country.