It was certainly hard to understand why Linington did not point to the spot in the seventh minute when Adam Reach's goalbound shot was handled on the line by Keogh.
Carvalhal and the rest of the Wednesday bench were furious and their sense of injustice deepened after Derby went ahead in the 17th minute when Christie bundled the ball in after Darren Bent had failed to connect with a corner.
Bent should have added a second two minutes before the break when his header flashed just over but the visitors continued to hammer on Derby's door in the second half.
Liam Palmer had a shot deflected inches wide before Fernando Forestieri fired over from 12 yards after Gary Hooper set him up. The Argentinean was foiled by a plunging save from Scott Carson on the hour but against the run of play, Derby scored again seven minutes later.
A Jacob Butterfield shot was deflected into the path of Pearce who beat Cameron Dawson from eight yards for his first Derby goal but Carvalhal knew it could have been so different.
"In my opinion, it's the worst decision in the Championship so far," he said. "I have seen nothing like it this season.
"It's so clear, I don't understand it. I have nothing against the ref, nothing against the person but the decision was very, very poor and it had a big impact on the game."
Carvalhal was spoken to by the referee but he insisted: "In that moment I was emotional but I didn't say any bad words, and I didn't do anything wrong in my opinion.
"I don't understand the decision. People talk a lot about how we need technology but why do we need a camera or a video when we have three referees on the pitch, one of them must see it. They have communication and can say it's a clear penalty."
Derby manager Steve McClaren agreed a penalty should have been given. "Keesy (Keogh) made a great save without his gloves on and we rode our luck in that," he said.
"Game's are turned on that one way or another and it turned our way and what you have to do in those instances is take advantage and that's what we did.
"It didn't stop Sheffield Wednesday playing the way they did, they kept coming forward and creating chances, but it was maybe the luck we didn't have last week we got this week. The ref has to make a snap decision and it went our way.
"It's a huge win, we said put a marker down at five o'clock and they've done that. There were aspects of the performance that improved immensely and we created chances as well."