Huddersfield ended a run of nine successive defeats with a battling 0-0 draw against their fellow relegation strugglers.
But one point could have turned into three but for Mason changing his mind over giving Huddersfield a penalty when full-back Florent Hadergjonaj tumbled.
Mason spoke to his assistant Stuart Burt before reversing his decision, instead awarding a free-kick to Cardiff for Hadergjonaj pushing Joe Bennett before the Switzerland international fell in the box.
“Everybody knows the referee gave a big decision that cost us the game,” said Huddersfield boss Wagner, who revealed that he had only spoken to Burt and not Mason after the final whistle.
“It was the most clear-cut chance of the whole game and they took it away from us.
“I know they (officials) have a very difficult job, but sometimes they make it much more difficult for themselves.
“The referee even gave them the ball. I have no clue what was in their head.
“After seeing the footage, it’s a clear penalty, but I don’t know how many decisions like this have gone against us this season.
“We will probably get another phone call from the FA apologising for the decision.
“Six weeks ago, our negative run started with one of the worst days for Michael Oliver against Brighton when he made a mistake.”
Huddersfield remain bottom of the table and eight points adrift of Cardiff.
Wagner had labelled the game “must-win” before kick-off and could take some comfort from the fact that his team were the better side.
But he added: “I said before we had to win it and we haven’t done.
“Clearly, we were the more active team and we deserved something - the spirit and attitude was there.
“But it shows how big decisions are important in this game. It’s something you can’t control.”
Cardiff manager Neil Warnock, perhaps not surprisingly, had a different take on the game’s main talking point.
Warnock felt Huddersfield should not have had a spot-kick and he insisted Cardiff should have had a first-half penalty when Hadergjonaj appeared to trip Junior Hoilett.
“It was a good job we had an experienced linesman because there was not enough contact for a penalty,” Warnock said.
“Thankfully, the linesman was well placed and was brave enough to see it for what it was.
“Junior Hoilett’s penalty shout was 10 times worse.
“How that can be two people with a genuine coming together over the ball, I don’t know.”
Cardiff failed to manage a single attempt on target in what was a poor display from the home side.
But Warnock said neither of his two frontmen, Callum Paterson and Victor Camarasa, were fully fit, saying: “They have helped me out.
“Camarasa has got a muscle injury from last week and Paterson couldn’t get around like he normally does.
“It would have been easy to have lost that game in the last few minutes.
“But that’s our sixth clean sheet, which is a good statistic. If you cannot win, then you get a point.”