Fernando Forestieri's penalty midway through the second half was enough to separate the teams in a thunderous Yorkshire derby played out in front of 22,368 - Huddersfield's biggest league attendance on this ground.
The hosts dominated possession and carved out a number of openings - particularly in the first half - but were unable to break down a stubborn Owls outfit who always looked threatening on the break.
"It's a disappointing result but I don't have any complaints about the performance, the effort, the attitude, the fighting attitude," said Wagner.
"If two strong sides play against each other then it's even - it's tight like it was today.
"One situation decided the game and unfortunately it was a situation for Sheffield Wednesday.
"I can accept this result because we performed good - not outstanding but good. This is Sheffield Wednesday, one of the top teams in this division, and we are able to be competitive against them."
Meanwhile, Wednesday boss Carvalhal was full of praise for front two Forestieri and Gary Hooper following a second away win of the season which boosts their own promotion aspirations.
"Fernando and Gary Hooper got everything they need to do very well, but like all good strikers they need something to make them click - Fernando's click was he played well and linked superbly with Hooper," he said. "I believe the future is bright with these two."