The 27-year-old faced five batters in the sixth inning of Sunday's 11-9 win over the Chicago White Sox and allowed one run. He came back out for the seventh inning and gave up hits to Alex Rios and Alexei Ramirez before exiting with the team trainer. He was charged with two runs on four hits over one-plus innings.
Blue Jays manager John Farrell said Perez will fly to Florida for further examination.
Perez is 2-2 with a 3.43 ERA on the season.
Toronto will not make a corresponding roster move immediately.