The Owls saw a four-game winning run brought to an abrupt halt as they suffered a first home defeat since November.
First-half goals from John Egan and Harlee Dean did the damage for Brentford, with Wednesday only having an injury-time goal from Fernando Forestieri to show for a second-half onslaught.
The Owls were adamant they should have had a penalty with the score at 0-0 when Forestieri went down under a challenge from Dean, while Carvalhal felt there was a foul in the build-up to Brentford’s second goal.
“The referee in the first half was a disaster,” he said. “A very poor performance, he made everybody nervous, he made the fans nervous, he made my players nervous and he made me nervous.
“He didn’t see a clear penalty, he didn’t see a block on (Vincent) Sasso for their second goal and there were a lot of faults and little things that made everyone nervous.
“I checked the video and it is a clear foul on Fernando.
“We can achieve a very good position, but the referee was very poor, these are the facts.
“I hope in the future we can achieve a good position, but I hope we have more luck. The referee was very, very poor, I am not judging, I am just talking facts.
“We played very poorly in the first half. We didn’t start well, but we played three days ago and Brentford didn’t.
“The second half, the Brentford goalkeeper was fantastic, he made some great saves. We fought a lot and made opportunities but we didn’t score. But I don’t want to give excuses.”
Brentford boss Dean Smith was delighted with his side’s attacking display at Hillsborough, as they continue to thrive in front of goal since the sale of Scott Hogan.
The Bees lost their top scorer to Aston Villa in the transfer window and have now scored nine goals in four games without him.
“We have looked like scoring in the few games, we have scored nine goals since Scott has gone and some of our attacking play has been really good in recent weeks,” he said.
“We knew it would be tough here but I thought first half we controlled it. We deserved to go in at the break in front.
“We had a number of chances in the second half to break and create better opportunities and when you don’t get that third goal, it leaves them thinking they can get something.
“They have missed some chances that they would expect to score and we have defended wilfully and in the end it took a piece of magic from Forestieri to get past us.”
On the penalty incident, Smith added: “I have seen them given and I have seen them not given. Forestieri went down easily a few times before and that might have been playing on the referee’s mind.”