The umpires didn't need long to overturn it, as the replay appeared to show that second baseman Danny Espinosa tagged Alonso around the shoulder just before his foot hit the bag.
"It's nice to have one go our way," Williams said.
Before the umpires reviewed the play, Padres manager Black came out to argue. Gyorko had already stepped back in the box and pitcher Rafael Soriano was on the mound when Williams ran out onto the field to challenge the call.
"There was some question from Buddy whether he had been in the box and they'd put the game back in play," Williams said. "I got out there as soon as we could determine whether it was an out call."
Earlier this season, Black attempted to challenge in a game, only to be told that too much time had passed and the hitter was already in the box and the pitcher was on the mound.
"My challenge wasn't allowed because the pitcher was on the rubber and the hitter was in the box and play was ready to resume," Black said of the April 2 game against the Dodgers. "I thought the same thing happened today.
"I took offense that it was allowed in San Diego and here it wasn't allowed. The umpires informed me it was at their discretion."
Jeff Seidel is a contributor to MLB.com. 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.