Second-base umpire Mark Ripperger ruled that Pena had beaten right-fielder Travis Snider's throw to shortstop Jordy Mercer, and avoided a tag.
Pirates manager Clint Hurdle came out to challenge the play which, following a review of one minute and 55 seconds, was overturned.
Zack Cozart followed with a double that scored Todd Frazier from third base for a 2-0 lead that would have been 3-0 if not for the successful challenge.
Tom Singer is a reporter for MLB.com and writes an MLBlog Change for a Nickel. He can also be found on Twitter @Tom_Singer. This story was not subject to the approval of Major League Baseball or its clubs.