The Magpies were left aggrieved by two key incidents in the match as Wigan boosted their survival hopes with a 2-1 victory.
The first incident saw Wigan striker Callum McManaman escape any punishment for a reckless knee-high challenge on Newcastle substitute Massadio Haidara, who had to be stretchered from the pitch.
That infuriated the Newcastle bench, and their annoyance was compounded in the 90th minute when Arouna Kone netted Wigan's winner after it had appeared that home defender Maynor Figueroa had handled the ball in the build-up.
Pardew told Sky Sports 1: "I'm disappointed for our team and for Wigan in a way, disappointing how it was conducted. The tackle was awful, and we've lost the game in the last minute to what I think is a handball, and also got a boy going to hospital.
"In all honesty it's difficult to take and difficult to talk about at this stage.
"All I would say is my team have put in an honest performance and actually we're very, very unlucky to come away with nothing.
"We also feel we should have had a corner before the goal. It's just unbelievable really, the decisions just seemed to go against us."
When asked how Haidara was, Pardew, who revealed referee Mark Halsey had apologised to him at half-time for missing the McManaman challenge, said: "Well it's not going to be good because the tackle was so bad. And that's the truth of it."
Wigan manager Roberto Martinez insisted McManaman was not a malicious player and said he would be apologising to Haidara.
"Remember it's Callum's full debut in the Premier League. I haven't seen the replay, I believe that he touches the ball and then it's a bad challenge, but it's nothing malicious, he's not that sort of boy," the Spaniard said.
"It's the normal enthusiasm that you get in your debut.
"I can't really comment too much because I haven't seen the action but I can guarantee that Callum McManaman is a young man full of talent and in his debut probably showed the enthusiasm that you expect, but he's not a malicious player."
Regarding an apology, Martinez said: "I think he wants to contact the player. I don't know if he's done it already but he will do that because when you get an injury in that manner you obviously don't want to leave any bad feelings.
"If Callum hasn't apologised yet then he definitely will do that because we're a football club where those values are very important."
Kone's controversial match-winner helped Wigan close to within three points of 17th-placed Aston Villa and safety, while they also still boast a game in hand on the three teams above them.
Martinez said he had not seen the handball but, if there was contact, was pleased to see his side benefit from some good fortune after seeing numerous decisions go against them this season.
"I haven't seen the replay (of the handball). If that's the case then I'm delighted because the whole season we've been on the back of bad decisions against us and in football sometimes you get a little bit of a break and sometimes you don't, and believe me all season we've had enough of no good luck going our way," he said.
Martinez was critical of the half-time melee which saw Carver try to confront McManaman, something which continued in the tunnel and resulted in Barrow also being sent off.
"I have not seen it but it is something which should never happen," he added.
"It is not for anyone to take justice into their own hands."
The controversy overshadowed what was a vital win for Wigan - their first at home since late November.
"It was a day that we knew we needed to start showing a different type of character at home," Martinez added.
"Our home form hasn't been good enough in terms the points we have collected not because of the quality of our play.
"We had to show an incredible character to get the winner and probably we got a little bit of luck, which is probably what we deserved because over the course of the season we've not been a lucky side.
"The reverse fixture at St James' Park we had a couple of really difficult decisions (Figueroa was controversially sent off) to take so it was really pleasing to get three points so late in the game."
Injured Newcastle - and former Wigan defender - Ryan Taylor expressed his dissatisfaction with McManaman's challenge on Twitter.
"Nothing to do with the scoreline an the fact it was a red but as a footballer it's the definition of a 'sh*thouse tackle'," he wrote.
"Wow. Not even a yellow #baffled."
After the Latics' controversial winner he added: "So Maradona has been teaching Figueroa a few lessons I see #Shocking"