Juan Mata opened the scoring six minutes from the end of a keenly contested first half at St James' Park through an excellent free-kick.
Pardew felt an offside call went against his team in the move leading up to Dan Gosling being penalised for a foul on Darren Fletcher - a verdict from referee Kevin Friend that Newcastle's manager believed was generous towards the Scotland international.
"I thought in the first half it was pretty tight - a little bit tense for both teams, trying to find their way," Pardew told reporters.
"The first goal, really and truly, was a tough decision on us. I thought it was offside and wasn't a foul either.
"When Mata scored I thought it settled United down and they looked a much better outfit after the goal.
"Unfortunately for us we just couldn't get into the game. The second goal was a mistake and then we had an uphill task in the form that we’re in."
Following their last-gasp 1-0 win over Crystal Palace a fortnight ago, Newcastle have conceded 11 unanswered goals in consecutive losses to Everton, Southampton and United.
Untimely injuries have taken their toll, although Pardew is hopeful of having top scorer Loic Remy available for the trip to Stoke City next weekend.
The Britannia Stadium assignment represents the penultimate match for which Pardew is banned from the touchline after he headbutted Hull City's David Meyler.
Newcastle have lost four out of five games since Pardew was punished by the Football Association, with the incident continuing to cast a shadow over the club.
"There’s no doubt that we're lacking a bit of cutting edge," Pardew added. "Loic's not far away.
"It would be a boost for all the squad if we could get him back in and around us - hopefully we can for Stoke because that's a big game for us.
"We've lost two games heavily at home, we lost at Southampton. We need to make sure we get back on track - we have 46 points. We need to push on if we can."