Papiss Cisse saw his effort midway through the first half hacked off the line by Winston Reid, with assistant referee Matthew Wilkes not convinced that the whole of the ball had crossed the line.
With fellow strugglers Aston Villa and Wigan both picking up vital away wins the decision could yet prove crucial at the end of the season and Pardew believes his team were hard done by.
"It was a great win for Wigan and it has put extra pressure on us and all those around us," he said.
"But you can only do what you can in a game and I thought we were terrific in the first half. I thought we had a legitimate goal that was chalked off.
"I thought it was in at the time. I saw the linesman slip over and it worried me because he is in line with that, and if he hasn't seen it.
"I asked him at half-time and he said he had seen it. I don't know how he did that. It was down to the referee then. I thought by West Ham's reaction it looked in. And sometimes player reactions tell you everything."
The controversy proved to be an isolated moment of excitement in a game with few clear-cut chances.
Despite the stalemate Pardew was pleased with the team spirit shown by his players on a week when their togetherness has been brought into question.
"In the second half our flair players faded, Hatem (Ben Arfa) in particular, unfortunately for us," he said.
"We lacked a little bit of punch. We had to roll our sleeves up in the last 15 minutes, defend well and the goalie play well, and dispel some of the stupid myths that have been thrown around about us - that there is a rift and a lack of unity.
"We put that to bed today, now we have got to show the quality in the group to get us out of this mess that we are in."
West Ham would have been the happier side with the draw as their top-flight status has not looked in jeopardy for some time.
Former Newcastle favourites Kevin Nolan and Andy Carroll had chances to win the game for the Hammers and assistant manager Neil McDonald felt they proved there was no chance of split loyalties for the duo.
"They are 100 per cent behind West Ham," he said.
"Obviously they have a past with Newcastle and good times with them but they are so focused on West Ham trying to get in the top 10 now with two games left, after getting newly promoted and they've been solid all the way through.
"They've contributed as much as anyone in the team which is fantastic."
McDonald, who also spent time at St James's Park during his playing career, has backed the Magpies to retain their Premier League status.
"I've said before, I think Newcastle have got enough to stay up," he added.
"But everyone is slightly still under pressure with the result that Wigan have had so everyone needs to do the best in the next game to try and get the points on the board so they can't be caught, but personally I think they will be okay."