Victoria Police were called to Almeida Crescent at South Yarra, close to nightlife on popular Chapel Street, about 11.40pm on Friday after reports a number of shots were fired at a man.
The 53-year-old from South Yarra - named in multiple media reports as Mohammed Keshtiar, a bikie also known as Afghan Ali - sustained life-threatening injuries in the attack.
He later died in hospital, while another man who was him was uninjured.
"It's important to know that (the uninjured man) isn't forthcoming at the moment with information to police," crime command Detective Superintendent Geri Porter said.
"This wasn't a random attack. We believe this was targeted."
The 53-year-old had been to the gym before he was fatally shot, police said.
Det Supt Porter confirmed police had identified "associations" with organised crime through their early investigations, but said it was unclear whether those associations played any part in Friday night's attack.
Following the shooting, police on Saturday morning found a torched car at Rowville in Melbourne's east, and believe it could be linked.
Det Supt Porter urged anyone who saw suspicious activity on or around Churchill Park Drive in South Yarra between midnight and 5am on Saturday to come forward.
"We're very concerned about not only the risk to the people or persons that are targeted, but also innocent community members that get caught up in activity like this," Det Supt Porter said.
"We have dedicated and committed investigators on this matter right now as well as ... specialist support units."
She could not say whether police were concerned about possible retaliation attacks.
CCTV was expected to play a crucial role in the investigation, Det Supt Porter said.
She urged anyone with information about the shooting to speak with police.
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