The incident happened in the third inning of the Cardinals' 11-3 rout at San Diego's Petco Park.
The Padres said the 6-foot-10 Young was admitted to Scripps Green Hospital in nearby Torrey Pines with a nasal fracture and a lacerated nose.
"When I hit it, I thought it was going over his head," Pujols told the St. Louis Post-Dispatch. "But it hit him right in the face. There was blood all over the place and I began to pray about it and make sure it was all right."
"If he weren't so tall, the ball would have gone into center field," Cardinals Manager Tony La Russa said. "It was one of those freak things."
Later in the inning, Padres catcher Josh Bard sustained a high left ankle sprain during a play also involving Pujols.