Black announced the Padres decision following a 4-2 loss to the Rockies at Coors Field.
"We just decided it was the prudent thing to do," Black said. "We'll take a step back and assess, draw up a game plan on his rehab."
Young tossed six scoreless innings in his season debut on Tuesday in Arizona and was to start the home opener on Monday at PETCO Park against the Atlanta Braves.
Kevin Correia will now start against the Braves.
Young first complained of tightness in his shoulder the day after his start in Arizona. The Padres have the option of placing Young on the disabled list retroactive to April 7.
The Padres likely won't need to fill Young's spot in the rotation until Sunday when they host the Diamondbacks.
Young said Saturday that his shoulder was feeling better. He told Black that on Sunday, as well.
"We have an opportunity to give it an extra rest. At this point in the season, it's the smart approach," Young said on Saturday. "It's nothing I'm worried about."
Black said a replacement for Young will come from within the organization, though he wouldn't say if that's from the 25-man roster or from Triple-A Portland.
Tim Stauffer has pitched well in long relief thus far, helping save the bullpen from work in Arizona with a two-inning stint, then hurling three scoreless innings in the Padres' 5-4 win in 14 innings on Saturday.
Left-handed pitcher Wade LeBlanc -- who pitched well during Spring Training -- and was the Opening Day starter for Portland, could be a candidate.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.