The 25-year-old said that the illness had sapped his strength, leaving him no choice but to rest and resume training prior to the start of the US Open on August 26.
"In Montreal (last week) I thought I just had a cold," the Austrian said. "But it turned into a fever yesterday.
"The smart thing is to not risk the US Open and the rest of the season, I need to get healthy and there are still 12 days to go before the start in New York."
Thiem's pullout leave the bottom half of the draw wide open after winner in Toronto Rafael Nadal also pulled out of Cincinnati, the last major tune-up prior to the final Grand Slam of the season.
Top seed Novak Djokovic and number three seed Roger Federer are both placed in the top half.