Howe's side were outstanding and were rewarded for their brilliant display when Harvey Barnes scored an 86th minute opener.
That looked set to give Newcastle an advantage to take to the Nou Camp for the second leg, but Yamal stepped up in the 95th minute after Malick Thiaw fouled Dani Olmo inside the box.
That sparked an angry reaction at full-time, with Joelinton making his frustrations known to substitute Anthony Gordon, who had conceded possession in the build-up to the penalty.
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Asked about the confrontation, Howe said: “I haven’t seen the goal again and it’s sort of a little bit unclear to me quite what happened. Sometimes you don’t get the fixed picture, so I’d need to see it again before giving you my opinion.
“But certainly as a team, we should have done better. We defended so well for the game, all through the game in different phases.
“The goal seemed soft. All I remember is a ball went through the middle of us and it should never happen at that stage of the game."
That momentary lapse came at the very end of what had been a stirring display from Newcastle.
Howe said: "A really good performance from the team, very, very good in all phases, really.
"I thought we limited them with a really good defensive performance from the team and I thought we attacked really well too.
“Although we didn’t create an abundance of clear-cut chances, I thought there were chances all through the game for us.
“It was great to see us finally score and then the last attack of the game, the last kick of the game, it’s a tough one to take."
Despite the last gasp penalty frustration, Howe said: “We have to believe we’re very much in the tie. The performance was very good, as I say.
"I thought we played well against them the first time and I thought the defeat was harsh on us. I think the draw is harsh on us again.
“But it shows their quality. If you switch off for a second, they will punish you and although I didn’t think they really looked like scoring today, there’s warning signs, they’ve got quality, they’ve got players who can hurt you in an instant, and that’s why I think our defensive performance was strong, so I’ really pleased with the players.
“Individually, I thought there was also some very strong performances today, which was great to see."