Toronto's right-hander was struck by a ball off the bat of catcher Russell Martin in the fourth inning. The sharp single hit Alvarez on the left shin, and he was immediately forced to leave the game.
X-rays came back negative as Alvarez was lucky to avoid any type of serious injury. His next start would be Saturday against Tampa Bay.
"He's good to go, but given how that swelled up immediately, there was no question we were going to get him out of the ballgame right then," Blue Jays manager John Farrell said of Alvarez, who allowed four runs on five hits in 3 1/3 innings before departing.
The 22-year-old Alvarez also narrowly avoided an injury earlier in the game when he stuck out his throwing hand to knock down a comebacker by New York's Eric Chavez.
Alvarez and left-hander Ricky Romero have been the sole members of the Blue Jays' starting rotation to remain healthy this season. Earlier in the year, right-handers Brandon Morrow, Kyle Drabek and Drew Hutchison were all lost within the span of four days because of various injuries. Morrow returned following a two-month absence on Saturday, but both Drabek and Hutchison are out for the year.
Left-hander Aaron Laffey came on in relief of Alvarez but lasted only 2 2/3 innings before he too was forced to depart with a left leg bruise. Laffey was hit by a hard grounder off the bat of Derek Jeter and felt his leg go numb, but he also received clearance and is only listed as day to day.