Canty was set to make his WorldTour debut in Adelaide but began to suffer from flu-like symptoms, including fever and chills, overnight.
After examination, the team and race doctors confirmed the virus and that he should not race. He will be replaced with New Zealander Tom Scully.
“It’s gone from starting a WorldTour race on my 25th birthday to being taken out of the race sick. Obviously, it’s disappointing, Canty said.
"I spent a fair bit of time preparing for this race, and I think my form’s quite good. It’s definitely frustrating, but it happens."
The Santos Tour Down Under will be Scully’s first race with the Cannondale-Drapac team.
“I would have liked to get a haircut and have a shave before my first WorldTour race," Scully said. "But at the end of the day there is nothing to worry about,”
“All I have to do is pin the numbers on tomorrow and get from point A to point B, supporting my new teammates along the way."
Team leadership remains unaffected with Mike Woods and Tom-Jelte Slagter serving as joint captains.
“We had to make a quick decision. For Brendan’s own health and his own sake, I didn’t want to put him in the race," sport director Tom Southam said.
"We came here to support Mike Woods and Tom Slagter, so the most important thing is to have a rider that’s 100 percent. It’s unfortunate it’s not Brendan."
Team Sky was also forced to make a last-minute change to its roster after another WorldTour debutant, British Olympian Owain Doull, was ruled out due to illness. He spot was taken by Kenny Elissonde.