The Caulfield shop of the Burgertory chain was destroyed by fire on November 10.
At the time, the owner said it was linked to his involvement in a pro-Palestine rally and labelled it a hate crime but police now say although the fire was deliberately lit there's no evidence it was racially or politically motivated.
Hours after the owner made the claim, two groups of about 200 people clashed near a synagogue and the Burgertory store.
One man was pepper-sprayed by police and another reported receiving minor injuries after being hit by a rock.
Police arrested two men on Wednesday before charging a 25-year-old man with arson, robbery, car theft and other offences on Thursday.
The man also faces charges over the alleged arson of a tobacco store fire in Bendigo on Monday which resulted in more than $4 million worth of damage.
The tobacco store fire is not related to the ongoing battle over illicit tobacco that has seen more than 30 shops firebombed.
He will appear in the Melbourne Magistrates' Court on Thursday.
Police have also charged a second 27-year-old St Albans man with arson and car theft.
He was released on bail pending his case at the Melbourne Magistrates' Court on Friday.
Victoria Police Inspector Scott Dwyer said the Caulfield incident was not a hate crime.
"It wasn't motivated by prejudice or politics," he said in a statement.
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