The Yankees announced the move Sunday, calling up infielder Thairo Estrada from Triple-A Scranton/Wilkes-Barre to take his place on the active roster.
Judge has what the team says is a "pretty significant" oblique strain, and there is no timetable for his return.
"Look, it's Aaron Judge," Yankees manager Aaron Boone said Saturday.
"He's one of the great players in the game, such a key figure to our club. Not only just between the lines, obviously, but what he means to us in the room. And he'll be part of continuing to lead us forward, as a group."
The injury to Judge took place while swinging at the plate during the bottom of the sixth inning in the Yankees' 9-2 victory Saturday over the Kansas City Royals.
Judge had hit his fifth homer of the season earlier in the game, and on the season is hitting .288.
Tyler Wade is expected to take Judge's place in the outfield while he is on the injured list.