The Blue Jays evaluated Shoemaker and confirmed he suffered a left knee sprain. He'll undergo an MRI on Sunday.
The veteran repeatedly slammed his fist into the ground in frustration while the training staff took a look at his injury.
Shoemaker was walking gingerly in the Blue Jays' clubhouse after the game, according to Ben Nicholson-Smith of Sportsnet, who also reports that manager Charlie Montoyo expressed hope the 32-year-old will miss just one start.
He held the Athletics scoreless on three hits before Sam Gaviglio replaced him.
Shoemaker was off to a terrific start to begin his time with the Blue Jays. He entered Saturday with a 3-0 record alongside a 1.75 ERA and 3.96 FIP in 25 2/3 innings.