Alvarez grounded out to first base in the first inning and was replaced at DH by Corey Julks when his turn came up again in the third.
Alvarez came in batting .274 with 17 home runs and 55 RBIs in 56 games.
The AL Rookie of the Year in 2019, Alvarez was an All-Star for the first time last season, when he hit .206 with a career-high 37 home runs and 97 RBIs.
The Associated Press contributed to this report.
Astros slugger Yordan Alvarez exits early because of oblique discomfort