Referee Andy Madley waved away appeals for a spot-kick for Trevoh Chalobah's 53rd-minute challenge on Anthony Gordon and was backed by VAR Peter Bankes, leaving the Magpies' head coach baffled.
Howe said: "Anywhere else on the pitch, that's a blatant free-kick. When it went to VAR, I thought, 'This is going to be overturned, it's a clear error.' It's as clear a penalty as I've seen.
"The defender only focuses on Ant [Gordon]. They said it's shielding, but I don't agree with that analysis. I'm really disappointed that wasn't given."
Newcastle, so poor in derby defeat at Sunderland last Sunday, roared out of the blocks and were 2-0 up inside 20 minutes, Nick Woltemade scoring from close range after keeper Robert Sánchez had blocked Anthony Gordon's shot and then doubling his tally with a neat finish from a Gordon cross.
But in a classic game of two halves, Reece James' 49th-minute free-kick dragged the visitors back into it and a much-improved second-half display yielded a point when João Pedro capitalised on Malick Thiaw's slip to level with 24 minutes remaining.
Howe said: "It's tinged with huge disappointment for us. I'm really disappointed for the players. We deserved to win that game, in my opinion anyway.
"The only real disappointment in the first half -- because I think it's the best we've played -- is that we weren't further ahead.
"We had the chances and played with real energy, intensity and quality. It was great to see us creating the big moments in the penalty box. It's a huge disappointment we haven't won the game with the effort we've given."
Opposite number Enzo Maresca, however, felt it was his side who might have left with all the points after responding with huge character in adversity.
Maresca said: "I think after the first half, they deserved to win the game, for sure. From my point of view after the second half, we deserved to win the game. This is my point of view.
"After the second goal we scored, we had three or four clear chances to score one more. They also had one with [Harvey] Barnes -- that is the only one I remember as a real chance -- but overall, I think the draw is correct."
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It has proved an interesting few days for Maresca, who has been linked with a potential vacancy at Manchester City should Pep Guardiola leave and also questioned the support he was receiving from the club.
However, when it was suggested he had endured a difficult week, he said: "My last week has not been complicated, it has been good. We beat Everton, we beat Cardiff and we drew with Newcastle away, so in terms of results, I'm happy.
"Again, there are things that for sure we can do better, but I think we're going in the right direction."
