Haidara was stretchered off at the DW Stadium following a challenge from the Wigan forward before the hosts snatched the win in the final minute thanks to Arouna Kone's strike.
"It was an awful tackle," Pardew told BBC Sport. "I have got a boy going to hospital and that's a worse feeling than losing.
"It looked a bad tackle but I didn't realise how bad until it filtered through to us."
The defeat has left Newcastle in 13th place in the Premier League table.