D-backs manager Kirk Gibson initially had a conversation with home-plate umpire Brian Gorman before heading out to second base to tell Rackley he intended to challenge the play.
After a very short review, the call was overturned, wiping Pagan off the bases.
Joe Panik followed the decision by drawing a walk before Buster Posey flied out to left to end the inning.
Steve Gilbert is a reporter for MLB.com. Read his blog, Inside the D-backs, and follow him on Twitter @SteveGilbertMLB. This story was not subject to the approval of Major League Baseball or its clubs.