The call by umpire James Hoye was overturned after a three-minute, 26-second review.
Carpenter scored during the ensuing at-bat on a single to right by Matt Holliday, who also went on to score during the Cardinals' three-run fifth, lifting St. Louis to a 7-0 lead.
"I applaud Carp's aggressive baserunning right there," Matheny said after the Cardinals' 8-0 victory. "That's a nice play and it would've taken a perfect throw, and almost did. It was almost a real nice tag, too. Fortunately, they saw that he didn't tag him and it worked out in our favor."
Matheny's record improved to 12-17 in challenges this year.
Daniel Kramer is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.