But Alonso quickly argued that he had tagged Santana and manager Bud Black issued a manager's challenge.
The umpire crew eventually overturned the call with the Padres clinging to a 1-0 lead.
Following the Santana play, Padres pitcher Jesse Hahn allowed a double to Brian Dozier and a walk to Trevor Plouffe. Then, with two outs, Kennys Vargas hit a three-run home run for a 3-1 lead.
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter. This story was not subject to the approval of Major League Baseball or its clubs.