Kai Havertz – who caught Dan Burn with a first-half elbow – scored an 89th-minute winner at Stamford Bridge this afternoon.
And Howe felt that his team, which hadn’t lost in the Premier League this year, was denied a second-half penalty after Jacob Murphy was brought down in the box by Trevoh Chalobah, who tugged his shirt.
“Could have been a red (for Havertz), but not going to shout from rooftops,” said United’s head coach.
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“But the penalty, with the use of VAR, I can’t understand that’s not been given, or the ref (David Coote) has not been asked to go to the monitor and review his decision. That makes a mockery of VAR.”
Howe added: “I can't look past the penalty, for me. Yeah, hugely disappointed with that decision, and how they have reached that decision. Basically, it's a penalty, Jacob's had his shirt ripped off his back near enough, goes down in the box, a clear penalty.
"Even if the referee doesn't give it on the pitch, I can kind of understand that, but then VAR doesn't give it, and they should at least make the referee review his own decision, because, if he does, he realises he's got it wrong."
On Havertz’s elbow on Burn, Howe said: "I think it could have been a red. I'm not going to sit here and say it should have been a red. I've seen it again, it could have been given.”
Reflecting on the 1-0 loss, Howe said: “Overall, it was a very good defensive performance, very strong tactically.
"Players were resilient to not give away too many chances, and I can't speak highly enough about our defensive display.
"Our pressing was good in the first half. We faded a bit in the second half, which is understandable, with the players we have out. We got too deep and they punished us.
"On the ball, we could have been better, but what has brought us these good results of late was our defensive endeavour, and that was present again today.”
Newcastle are 14th in the Premier League table and nine points above the relegation zone.