The 31-year-old who last played at Wimbledon six weeks ago, was to have started against former No. 1 Ana Ivanovic. Williams stands 34th on the WTA after months of injury absence.
The senior Williams had been intent on playing, arriving in the Canadian city with her sister Serena. "I was really excited to play Toronto," said Williams. "I came here ready to go and was practicing.
"I wasn't feeling very well and had to see the doctor today. I was diagnosed with a viral illness and unfortunately am unable to play. I am extremely disappointed. I'm very sorry to the fans and tournament."
Williams is replaced in the draw by Chinese qualifier Zhang Shuai, who will now meet Ivanovic, a semi-finalist at the San Diego WTA event