The Toon's win came courtesy of an injury-time winner from Papiss Cisse.
Pulis was a disappointed man as he left St James' Park, claiming his side should have had a free-kick seconds before Cisse struck, and that the goal had come after stoppage time had elapsed.
Pulis said: "The disappointing this is, if you look at the video, we thought we should have had a free-kick outside their box with a minute to go - well, there was 20 seconds to go - and then they come down and they score, which is over time.
"In the first half, he [referee Lee Probert] played, I think, a minute and 40 seconds over time and the second half, I think it's 3.40 when they score the goal.
"The fourth official said it was time when [Mike] Williamson actually handballed it - if he handballed it - so from them going down the bottom, I think it was 40 seconds."
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