The 21-year old striker, in his first Premier League start, produced a horror tackle on Massadio Haidara which forced the Frenchman off on a stretcher as the Latics edged the Magpies 2-1 at the DW Stadium.
Pardew felt McManaman should have been sent off and was also reeling as his side did not receive a free-kick for handball just before Arouna Kone's 90th-minute winner after Davide Santon had cancelled out Jean Beausejour's opener.
"It is an awful challenge. The pictures speak for themselves," said Pardew.
"I thought it was a bad challenge and I was 60 yards from the incident.
"The players knew because they were on top of it and there was a lot of bad feeling about that incident when it goes unpunished.
"He (Halsey) said 'If I've missed it I apologise' - that was at half-time.
"If it goes unpunished it doubles the impact on the mentality of the players and the team and it did have an impact on us, you can't get away from that.
"My job was to calm the players at half-time, not go looking for retribution, and try to win the second half - which to all intents and purposes we did.
"But again there's a decision at the end where we should have had a corner, it goes up the other end and there's a handball - that is tough to take.
"The linesman is looking right at it, the referee is there and all our players reacted and in that split second we didn't clear the ball - that's what happens when you miss a decision as big as that."