Encarnacion's middle finger has been bothering him for a while, and he aggravated it on a swing Saturday. The first baseman and designated hitter was rested Sunday as second-place Toronto tried for a three-game sweep of the AL East leaders.
Blue Jays manager John Gibbons hopes Encarnacion will feel better after the team's off day Monday.
Encarnacion was batting .251 with 21 homers and 64 RBIs. He had reached base safely in 16 consecutive games, and is 5 for 10 with a home run against Masahiro Tanaka, the scheduled Yankees starter.
Pennington was in uniform and available off the bench.