The Australian joins Britons Dan Evans and Johanna Konta in withdrawing from the Games due to coronavirus.
The Australian Olympic Committee confirmed the development following a press conference given by Australia’s Chef de Mission Ian Chesterman in Tokyo.
“We’re very disappointed for Alex. He’s said that he’s shattered, not being able to come,” Chesterman told reporters.
“It’s been a dream since he was a child to represent Australia at the Olympic Games, but he has sent his very best wishes for the rest of the team.”
Chesterman said the Australian No 1 returned two positive tests in Spain before he was due to fly to Japan.
De Minaur was knocked out of the singles at Wimbledon in the first round last month.