He tried to take batting practice in the cage at PNC Park before the game, but still was sore.
"We were hoping he was [ready to start], but we don't want to risk anything. He felt it in his oblique and nursed it yesterday a little bit," Murphy said.
"We just decided, precautionary, that this wasn't the best day to go. Hurts us a bunch, but that's part of it."
Murphy said Upton mentioned that he might have re-aggravated his oblique during Tuesday's 3-2 loss to the Pirates, though he wasn't sure if it came on the catch of McCutchen's ball.
Upton, who Monday was named as a reserve to the National League All-Star team, is currently considered day to day. Murphy is hopeful that won't lead him to a disabled list stint.
"I don't foresee that right now. But we don't want to reaggravate it," Murphy said. "That's part of the thinking for keeping him out today. We've got a day off tomorrow, and hopefully that can be the end of it."
Upton is hitting .259 with 14 home runs, 46 RBIs and 16 stolen bases -- leading the Padres in all three categories.
The Padres are off on Thursday before opening a three-game series on the road against the Rangers. He'll get Thursday to rest the oblique. The first half ends following Sunday's game.
Murphy didn't know if this injury would keep Upton from playing in Tuesday's All-Star Game presented by T-Mobile in Cincinnati.
Prior to the game, the Padres reinstated right-handed pitcher Dale Thayer and optioned lefty Frank Garces to Triple-A El Paso. Thayer has been on the disabled list with a strain of his right shoulder since June 17. He made on Minor League rehabilitation appearance last Saturday for Double-A San Antonio. Garces had a 3.81 ERA in 31 games but has allowed five earned runs in his last eight appearances.
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.