Scutaro left Sunday's game at Tampa Bay in the sixth inning after he felt something pop in his sore heel while charging a grounder.
Scutaro, 33, has been bothered by heel pain since late July. Monday's MRI revealed a tear in his plantar fascia, a band of thick tissue in the foot.
John McDonald started at shortstop against Baltimore on Monday night, with manager Cito Gaston saying Scutaro was unlikely to return for Toronto's final 13 games.
Playing every day for the first time in his career, Scutaro has posted career highs in average (.282), home runs (12), doubles (35) and walks (90) and has matched his career high in RBIs (60). He is eligible for free agency following the season.
The season may also be over for left-hander Scott Downs, who injured his right hamstring covering first base at New York on Sept. 16. Downs (1-3), who has nine saves and a 3.09 ERA, is still day to day, but Gaston said there may not be enough time left for him to return.
Left-hander Brian Tallet, who started Sept. 16 and left after two innings when he took a line drive off his right foot, is expected to make his next start Tuesday against the Orioles, Gaston said.