The Magpies manager was infuriated by the Wigan midfielder's challenge on left-back Massadio Haidara, who was taken to hospital as a result of his knee injury in their 2-1 defeat
The tackle occurred during the first half of Magpies' 2-1 defeat at the DW Stadium as the 21-year-old caught the left-back on the knee with his studs. Referee Mark Halsey did not see the incident, and McManaman escaped sanction.
"I'm disappointed for our team and Wigan in a way," Pardew told Sky Sports. "It was disappointing the way it was conducted.
"The tackle was awful and I've lost the game in the last minute to what I think is a handball and also I've got a boy going to hospital.
"It's not going to be good because the tackle was so bad. That's the truth of it."
Pardew admitted he went to see Halsey at half time, he said: "He apologised to say that he missed it."
The Newcastle boss also felt Arouna Kone's winner should have been ruled out due to a handball by a Wigan player in the build-up, and says that both the referee and the linesman should have spotted the infringement.
When asked if the assistant should have seen the incident, he said: "Yes. I also feel that you could tell by the players reactions because we all appealed as soon as it hit his hand.
"In that split second our clearance wasn't clear because we reacted. It tells it all as a referee, you should know that there's a handball there.
"We saw two teams who were really committed there and in all honesty it's difficult to take and talk about at this stage.
"What I will say is that my team has put in an honest performance and they are very unlucky to come away with nothing."