The Scottish veteran suffered an unspecified injury to his left knee while going after a shot in Wednesday's play at Rexall Center in Toronto.
Murray was the No. 2 seed in the tournament and is a two-time champion. He had been scheduled to play 16th-seeded Milos Raonic of Canada Thursday. Raonic was waved on to the quarterfinals.
The washout means a full singles schedule Friday with the completion of the third round followed by quarterfinal play in the afternoon and evening.