The visitors went one goal up through Oussama Assaidi's excellent opener, but an incredible first half culminated with two Stoke men - along with boss Hughes - being sent off by Atkinson.
Loic Remy's deflected effort put Newcastle in on level terms at the break, perhaps undeservedly. The numbers game certainly showed in the second half, however, as Pardew's men scored four goals without reply to record a Boxing Day hammering for Stoke.
Atkinson's decisions left many confused, and Hughes was no different as he pinpointed the referee as the reason for his side's heavy defeat.
Talking to Sky Sports, Hughes said: "We're dumbstruck by the performance of the referee, unfortunately.
"People say he's one of the best referees in the league, and he's performed worse than the standard required today."
Hughes went on in his stinging criticism, first sharing his opinion on the sending off of Glenn Whelan for two yellow cards.
"Apparently, he said that Whelan kicked the ball away, which bemuses me as Cabaye went over the top and Glenn reacted.
"Two minutes later he receives the second. An experienced referee should get the two players together and tell them to calm down.
"I'm dismayed by his performance. When you're on a yellow card you have to be careful, but Glenn's just as bemused as everybody."
Hughes went on to discuss the penalty decision in the first half, as Marc Wilson received a straight red card for fouling Remy.
"I'm assuming it's for denying a goalscoring opportunity. My view is that there's a lot of pushing and pulling.
"He went down very easily, but nobody seemed surprised when the penalty was given."
Hughes himself was sent to the stands for his reaction to Whelan's sending off, and was more apologetic for his actions after throwing his coat into the air and storming down the tunnel.
"I apologise as I kicked the ball onto the pitch.
"You have to accept that, but I think everybody who made the long trek to watch us today was disappointed with what happened."
Stoke were one goal up and looking comfortable before having Whelan and Wilson sent off in quick succession, and Hughes was more than happy with his side's performance.
"We played really well, and could have scored more.
"Newcastle were struggling to stay in the game and keep up with us, before the referee made some decisions which changed the course of the game to our detriment."
Stoke will now look forward to another long trip at the weekend, this time to London to face Tottenham.
"We've got a big game on Sunday against Tottenham, and in the end we have to try and protect players.
"Going down to nine men here means we'll be physically tested.
"We have to put this one behind us.
"We were on our way to maximum points, but we have to dust ourselves off now."
Danish keeper Thomas Sorensen started the game in the place of Asmir Begovic, who Hughes announced had broken his finger in training on Friday.
The Potters' boss confirmed that the Bosnian shot-stopper faced a prolonged spell on the sidelines after the game.
"Asmir's got a bad break of the finger. He's possibly looking at five to six weeks out."