Ellis had played in all five games for the Athletics so far this season, batting .211 with no home runs and four RBIs. Andy LaRoche replaced Ellis at second base.
A nine-year veteran who has spent his entire career with Oakland, Ellis started feeling discomfort during Thursday's 5-3 defeat. He was expected to be checked out by a Blue Jays team doctor.
Manager Bob Geren was unsure whether Ellis would be healthy enough to fly with the team to Minneapolis after Thursday afternoon's game. The Athletics open a three-game series against the Twins on Friday.