The right-hander experienced pain during a throwing session Saturday, and is scheduled to have surgery.
Blue Jays manager John Farrell says Sunday he hopes Santos will be back by spring training.
Santos, acquired in an offseason trade with the Chicago White Sox, has been on the disabled list since April 21. No date has been set for his surgery, and the exact nature of his injury was not disclosed.
Santos, 29, had recently begun throwing again at Toronto's spring facility in Dunedin, Fla. He was 0-1 with two saves and a 9.00 ERA in six relief appearances.