"Little soreness in his calf today," Green said. "As hard as he's pushed this year, as soon as he said that, we weren't going to push him at all. He's been out there grinding every single day."
It's unclear how Margot sustained the injury, but he informed Green after he grounded out to short in the top half of the frame.
Margot was replaced in center field by Matt Szczur on Wednesday night, and Szczur is slated to get the start there on Thursday as well. In Margot's absence, Szczur singled, walked twice and scored twice, as the Padres rallied from a four-run deficit.
Margot, who has developed into one of the Padres' most exciting players, is hitting .259/.305/.389 this season, while playing an elite center field. Before he graduated from MLBPipeline.com's top prospects list earlier this month, he was ranked as the Padres' best youngster.
Margot, who came to San Diego from Boston in the Craig Kimbrel trade, also missed time during Spring Training with knee soreness, but that was his left knee.
AJ Cassavell covers the Padres for MLB.com. Follow him on Twitter @ajcassavell. This story was not subject to the approval of Major League Baseball or its clubs.