The Magpies boss believes that the official made three mistakes during the match, which cost his team dearly.
"Two big decisions went against us and that was crucial in the result," Sky Sports News quotes Pardew as saying.
"The first one was a penalty, no doubt in my mind about that. I felt that at the time and my players' reaction told me everything I needed to know, and that should have told Howard as well.
"It hit his arm and it's going in the back of the net. That's a penalty isn't it?"
Addressing the Shelvey incident, Pardew said that he is "disappointed" in the former Liverpool midfielder as he is a player that he admires.
"Looking at video highlights I think that was disappointing for Jonjo as I think he is a terrific lad and that's unlike him, but again maybe you could argue he should not be on the pitch," he added.
Newcastle are back in action this Saturday when they travel to Old Trafford to take on Manchester United.