Josh Collmenter will start in place of Skaggs.
Manager Kirk Gibson made the announcement following his team's 4-2 loss to the Rockies and said that he would outline his reasons Tuesday.
"They're going to shut me down for the rest of the year," Skaggs said. "Body feels fine, arm feels fine, it's just a front-office decision. I wasn't happy about it, but it is what it is."
After three strong starts to begin his Major League career late last month, Skaggs' last three outings have resulted in a 10.50 ERA and some have raised concerns about his velocity being in the upper 80s towards the end of his last start as opposed to the low 90s he hit earlier in the game.
Still, as recently as Saturday, Gibson and pitching coach Charles Nagy both said there were no plans to shut Skaggs down.
While he would like to keep pitching, Skaggs admitted that he knew the decision was made with his best interests in mind.
"It's a good thing," he said. "Everything feels fine and it's their decision so I'm going to stick with it and trust the organization and trust the coaches and it is what it is."