Joe Willock canceled out Vitinha's opener for PSG, with Toon goalkeeper Nick Pope also saving Ousmane Dembele's penalty after Lewis Miley's hand-ball.
Pope's save came before PSG captain Marquinhos escaped a hand-ball call himself.
Asked what decision frustrated him most, Howe said: "Probably the one that wasn't given for us.
"You can berate the first decision, but if you think that is a penalty, which the officials did, for me, the next one has to be a penalty as well.
"I don't think the first one is against Lewis. It hit their player's arm first, and I just think it is unintentional. I know his arm is slightly detached from his body, but for me, there is no intent there.
"It is the consistency then that you want to see followed through. That is why I think credit to the players as we did not allow that to become a feature for us in the game, we focused on football which was a tribute to our mindset."
On the result and reaching the play-offs, Howe continued: "Really good resilience, character and quality. We had to deal with a lot today.
"Certainly the penalty decision against us was really harsh. We had to handle that and it was big for us. They were an outstanding team as well."
Newcastle now face a play-off against either Monaco or Qarabag. Howe added: "We wanted to win tonight, we didn't want the extra games.
"But we'll take it. We went down that route in the best possible way with a great performance against the holders. There's a lot to be positive about."