Cliff Pennington, who started at shortstop on Tuesday night, was originally the starter at shortstop on Wednesday as well, but Gibson sat him because Pennington jammed his hand when Padres shortstop Everth Cabrera slid into second on a double in the first inning of the Padres' 4-3 win on Tuesday.
"It's one of those deals, you get in the game and something else happens and you're kind of on the edge, and I got to take you out of the game," Gibson said. "He can still play in the game if he needs to play, but we made the decision to remove him [from the starting lineup]."
Owings has played the majority of innings at shortstop this season. The rookie started the season hot, garnering National League Rookie of the Month honors for April.
But May has not treated Owings well. Going into Wednesday's contest, he was hitting .197 in May, down 116 points from his .313 mark in April. His on-base percentage has also fallen precipitously, from .367 in April to only .228 in May.
"Just a lot of things that are going on," Owings said. "You hit balls hard right at people, missing some pitches, get pitches on the corner, get some bad calls. Just everything's coming into effect."
Despite his slump, there is a bright spot for Owings when he steps up to the plate at Chase Field. In 24 games at home, Owings is hitting .361 and has a .924 OPS.
"He had a tough road trip and then probably started pressing a little bit," Gibson said. "That's kind of why I was going to keep him out for two days.
"He'll be fine. He's been through it before in the Minor Leagues ... He's just got to learn how to trust himself."
Steve Gilbert is a reporter for MLB.com. Read his blog, Inside the D-backs, and follow him on Twitter @SteveGilbertMLB. Adam Lichtenstein is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.