The Magpies manager was infuriated by the Wigan midfielder's challenge on the left-back and revealed that referee Mark Halsey had apologised for missing the tackle
"[Haidara's] on his way to hospital," Pardew told the BBC. "It looks like knee ligaments and he's got terrible bruising on his leg as well.
"Obviously [the tackle] was right over the other side [of the pitch]. It looked a bad challenge but I didn't realise how bad until it filtered through to us from the sideline."
The 51-year-old admitted that Kone's winning goal, which came after Maynor Figueroa appeared to handball, had compounded a disappointing afternoon for his side.
"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. [The referee] apologised to say that he missed it."
Pardew believes the reaction of his players to Figueroa's handball should have made it clear to Halsey and his assistants that there had been an infringement.
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"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."