Tennis Canada said in a statement that the 29-year-old Czech star's withdrawal would mean former world No 1 Serena Williams is now given a top eight seed.
Venus Williams will take the available space in the main draw while a wild card spot would be handed to Svetlana Kuznetsova.
Kvitova said in a statement she had pulled out after the left arm injury that forced her to withdraw from the French Open flared up again.
"I'm so disappointed to have to withdraw from the Rogers Cup," Kvitova commented.
"My forearm injury is continuing to cause some problems so, on the advice of my medical team, I have made the decision not to travel to Canada."
Despite pulling out of Roland Garros, Kvitova went on to play Wimbledon, advancing to the last 16 for the first time in five years where she was eventually knocked out by Johanna Konta.
Kvitova has made a remarkable comeback to tennis after being attacked during a home invasion and robbery in 2016 which left her with serious injuries to her left hand.
Although doctors feared she may never play tennis again, she returned to the sport in 2017 and has since won eight titles, as well as reaching the final of the Australian Open in January.