The Magpies boss insisted that both strikes were not offside and criticised the officials following the 0-0 draw in the first leg of the round-of-32 contest.
"Both goals are onside and fundamentally the officials got them wrong," BBC Sport quotes Pardew as saying.
"It was a great game, Metalist are a good side and we played a great game tonight, we were physical and technical enough and in these games those are the margins.
"I can accept one but twice is tough to take. The law says it should favour the striker and both those decisions were level."
The teams go into the second leg all square despite Papiss Cisse having the ball in the net twice on the night.