Due to Federer's withdrawal, Canada's Milos Raonic now moves into the No. 16 seed position and will receive a first-round bye.
The draw to determine first-round match-ups will take place on Saturday.
The Rogers Cup run from Saturday through Aug. 12 at the Rexall Centre in Toronto.
Federer says he's disappointed to have to withdraw from the Toronto tournament.
Federer blames his withdrawal on having played in numerous tournaments recently.
"After a long stretch of tournaments, I will need some time to recover," said Federer.
"I look forward to coming back to Canada next year."