Werth, however, remained seated at second base and manager Matt Williams came out of the dugout to challenge the call.
Replays appeared to show that while the throw beat Werth, Gyorko did not apply the tag until after Werth's foot had touched the base. After a review of 1 minute, 47 seconds, the umpires overturned the call, ruling Werth safe on the two-base error and forcing the Padres back onto the field.
Williams is now 2-for-6 on challenges as Washington manager.
Elliott Smith is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.