Boone confirmed Tuesday that Stanton has a Grade 1 hamstring strain, an injury with a "reasonable" recovery timeline of three to four weeks.
Boone noted that Stanton is still in the "early days" of his recovery and said he's "hurting" for the injury-plagued slugger.
"I'm hurting for him," Boone told reporters, according to MLB.com. "I know what he's done to be here. His play speaks for itself. Hopefully it's something that doesn't end up keeping him down too long."
Stanton was placed on the 10-day IL on Sunday. The former National League MVP was limited to just 18 games last season because of multiple injuries but was off to a good start this season, batting .293 with three home runs in his first 14 games.
New York promoted former top outfield prospect Clint Frazier from its alternate site Tuesday, and Boone previously indicated the Yankees would use a variety of players to replace Stanton as their primary designated hitter.