Skaggs had been slated to start against the Rockies at Salt River Fields, but fellow prospect Trevor Bauer will instead get the nod.
D-backs manager Kirk Gibson said Skaggs informed the training staff Thursday of the tenderness and that by Friday he was feeling better. Still, the team decided to err on the side of caution.
"It's really us," Gibson said. "He's probably fine, but I just know he's going to out there tomorrow on Opening Day and be jacked up. I appreciate him telling us about it. It's gone away immediately, they worked on him and he felt great today."
Skaggs will throw a bullpen session Sunday.