He was taken to hospital in Athens, where he was disconnected from life support Friday.
The decision was made by family as Doujon's condition did not improve.
Doctors said he had been "clinically dead" since yesterday.
General director of the Henry Dunant hospital, Maria Kairi, said Doujon's family had decided to donate his organs.
His heart will go to an Australian national currently hospitalised in Athens' Onassis Cardiac Surgery Centre.
"They have also accepted to donate the rest of his organs to save Greek people," Kairi said.
Police have arrested four employees of a nightclub, reports news.com.au.
Zammit was among six Australians involved in a confrontation early on Tuesday morning with four staff at the Tropicana club on Paradise Beach, a well-known summer hotspot.
The Australians were suspected of having stolen bags and wallets in the nightclub, an accusation later dismissed by police.
The 25-year-old main suspect was initially charged with aggravated assault and impersonating a police officer, while three others were charged with complicity, judicial officials said on the nearby island of Syros.
The more serious charge was likely to change to manslaughter or murder after Doujon's death.
The stunned Greeks begged forgiveness and spoke of shame that it happened in their country.
Oliver Zammit told Greeks they had a "lovely culture and a great country" and the attack on his 20-year-old son was "bad luck", sparking an outpouring of grief.
"I would like you to know that this is going to tie myself and my family ... to Greece," Oliver told journalists as he fought back tears.
"His father humbled us all, it is all we talk about here in Athens ... This is not us, not this savagery," Anna Houliara wrote on a Facebook page for Doujon.
Another young Greek woman wrote: "I saw Doujon's father and I was shocked because he is a real human ... forgive us."
Almost 3000 people, many of them friends and family of the former Cecil Hills High School leader and Cabramatta League's Club worker, joined the tribute site.
"Our thoughts and prayers go to you and to your brave dad, Doujon ... condolences are simply not enough. Shame on all of us, shame on Greece," Isaac Valavanis said.
The bashing by bouncers who were masquerading as police on Mykonos has sparked political fallout.
Tourism Minister Aris Spiliotopoulos has set up a committee to clean up the tourism sector in the wake of the attack.
"As people, as citizens, as Greeks, we mourn the loss of a life. And as we talk about Greece's image abroad, it is logical that these isolated incidents sadden us even more," Spiliotopoulos said.