The Potters boss was aggrieved at match official Robert Madley's decision to book midfielder Steven Nzonzi for a second time eight minutes into the second half of his side's 1-0 Barclays Premier League defeat at the Stadium of Light and accused Jozy Altidore, his victim on both occasions, of making the most of minimal contact.
Hughes, who saw Glenn Whelan and Marc Wilson dismissed during a 5-1 defeat at Newcastle on his last visit to the north-east on Boxing Day, said: "We are disappointed, obviously, that a performance of real character and desire and determination and no little skill has got no reward.
"Unfortunately on too many occasions this season, we have been hurt by refereeing decisions that have had a marked effect on the outcome of the game.
"We are talking once again about a situation that I feel was a poor decision from the referee.
"It was difficult for him because I felt the lad Altidore went down very easily looking for an advantage and I felt on the night, too much of that was going on, to be perfectly honest.
"The referee has got to be able to look through that and understand what is happening. He wasn't very good in that regard and as a consequence, he bought a challenge where there was very minimal contact.
"The lad went down easily and the referee deemed fit to give Steven a second yellow card for that challenge, which is unbelievable from my point of view.
"I was really pleased with how we played, but there are too many occasions where we are having mountains to climb to enable us to win football matches.
"All we ask is that we have a level playing field and the key decisions are made correctly because when you have two sides going against each other, you want the best team to win and unfortunately, the best team didn't win."
Adam Johnson's 17th-minute strike was enough to hand Sunderland a win which, coupled with West Ham's failure to emerge from their trip to Chelsea with an unlikely victory, lifted them out of the bottom three for the first time since August.
However, they needed a superb 39th-minute save by keeper Vito Mannone and then six minutes from time, the crossbar to deny Ryan Shawcross an equaliser.
Asked if it felt like a big moment, first-team coach Charlie Oatway, standing in for the unwell Poyet at the post-match press conference, said: "Yes, it does.
"Since we came in, you could see the strain on people's faces in and around the club, and it's such a big achievement for those people as well as the fans and the players.
"They have to put up with it as well and keep hoping that we get out of the trouble that we are in, so it will be nice to go in tomorrow and see, hopefully, some smiling faces.
"I don't know how long it's going to last because of the games we have got coming up, so it's going to be tough. But it will be nice to see their faces.
"We have done well of late. We have got a style that we want to play, we are managing to get points and we have managed to claw it back, so to tick another box of winning at home, it's a good achievement for everyone."
Sunderland midfielder Lee Cattermole was conspicuous by his absence, sparking fresh speculation over Stoke's reported interest in him, but Hughes insisted no bid had been tabled and Oatway confirmed that.
He said: "He just had a little bit of a knock. There have been no bids."
Meanwhile, Argentinian striker Ignacio Scocco watched from the stands as he closed in on a move to Wearside.