Sappelt's liner appeared to have glanced off Storey's right shoulder before hitting him on the right side of his neck or head.
Storey fell to a knee and grabbed his jaw area as Astros personnel rushed to check on him. He was down for several minutes before walking into the Astros dugout.
Jose Valdez replaced Storey. The Cubs lead 3-0.
A week ago, Oakland pitcher Brandon McCarthy was hit in the head and needed surgery to fix an epidural hemorrhage, brain bruise and skull fracture. He was released from the hospital on Tuesday.