A record 35,268 gallery goers voted in the 2022 award, the highest number since the prize was first offered in 1988.
It's Eden's second consecutive year as an Archibald finalist, and he said he was ecstatic to discover he'd won the popular vote.
"This painting is one I have been thinking about and wanting to make for 10 years," he said in a statement.
The Sydney-based artist first met Johnson in 2021 while the actor was recovering from a near-fatal car accident, and the pair bonded over their shared experience of losing close family members to cancer.
Eden's mother Annette died from the illness in 2008, while Johnson founded the cancer charity Love Your Sister with his sister Connie before she died in 2017.
The winning portrait depicts Johnson holding a photo of Eden's mother, after the actor encouraged Eden to include his personal story in the portrait too.
The painter flew to Melbourne for a live sitting with Johnson, then worked six hours a day for 10 weeks to finish the portrait.
"The people have spoken and they loved Jeremy the most," Johnson said in a statement.
"He is an extraordinary storyteller, has a huge heart and he deserves this acknowledgement so fully."
The announcement was made at the Art Gallery of NSW on Wednesday.
Love your Sister has raised more than $15 million for cancer research.
The Archibald, Wynne and Sulman prizes are on show at the AGNSW until August 28, and the Archibald finalists will tour regional Victoria and NSW until July 2023.
23°C