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."