Söderling, a two-time French Open finalist ranked sixth in the world, was to have made his 15th consecutive Grand Slam appearance.
“He feels awful,” his agent Nina Wennerström told the TT news agency newspaper.
“He’s got a headache and stomach pains. The doctor things it may be a virus related to a throat infection.”
The 27-year-old Swede was enjoying a banner year on the ATP tour with titles in Brisbane, Rotterdam, Marseille and Båstad.
He had never previously won more than two titles in the same year.
“He simply felt too poorly to play a five-setter in a Grand Slam tournament,” said Wennerström.
Lucky loser Da Silva will take on Irish qualifier Louk Sorensen.
Sorensen takes the court a day after countryman Conor Niland, feeling the effects of food poisoning, lost an abbreviated match to world number one Novak
By advancing into the main draw from qualifying Sorenson and Niland made history by giving Ireland multiple representation in a Grand Slam men’s singles field for the first time.