The Russian right-hander's withdrawal was announced on the tournament's Twitter feed, which added that Romania's Simona Halep had now been elevated to second seed.
World number one Serena Williams will be chasing her fourth Rogers Cup crown after wins in 2013, 2011 and 2001.
Five-time Grand Slam tournament winner Sharapova, beaten by Williams in this year's Australian Open final and the Wimbledon semi-finals, has never won the Rogers Cup.
The hardcourt tournament is one of several tune-up events leading into the US Open, where Williams will be attempting to complete a calendar year sweep of all four tennis Grand Slam events.
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