PNE saw two strong penalty claims turned down by referee Chris Kavanagh, the second of those late in stoppage-time when Jermaine Beckford was felled in the box.
A draw would have been fully deserved but it was the Magpies who returned to Tyneside with the 2-1 win.
Lilywhites boss Grayson said: “We were disappointed with the outcome because we deserved so much more.
“It could have been one or three more points to the total we have collected from a tough schedule of games.
“There were a lot of encouraging signs, with good work off the ball and a lot of good stuff with the ball.
“It was a totally different game to when we lost 6-0 at Newcastle in the cup last week.
“Playing Newcastle with 10 men, as was the case at their place, would be a very difficult job for anyone.
“On Saturday we were brave, we went 4-4-2 against a strong team.
“We knew we had to have an intensity with and without the ball and we had that.
“Although we should have taken something out of the game, we can take heart from that performance.
“You look at Newcastle’s two goals, they only came from half mistakes from us but they have the players to punish you.
“I thought our back four was outstanding in the way they contained some good players.
“The midfield stopped Jonjo Shelvey from playing, all over the pitch you could not fault anyone.
“I’m just disappointed that the players did not get the rewards they deserved.”
Grayson was fuming that North End were not awarded either penalty they claimed for.
Callum Robinson got a push in the back just before the visitors scored their second.
Right at the death, substitute Beckford went down under a challenge from Grant Hanley.
Asked if the second one was a penalty, Grayson said: “One hundred per cent it was.
“Jermaine got on the wrong side of Hanley and he has gone to kick it without knowing Jermaine is there.
“Hanley kicked his backside and put him on the deck. Callum Robinson’s was a penalty as well, he has been pushed in the back.”
Grayson condemned an unsavoury incident during stoppage-time when coins were thrown at Newcastle’s Deandre Yedlin from the Town End.
He was being bandaged up behind the goal after cutting his head in a collision with PNE sub Simon Makienok.
Yedlin’s injury was caused by the clash of heads rather than the coins, but it does not reflect well on the club and CCTV will be used to try and identify the offender.
Said Grayson: “Obviously something was thrown and you don’t want to see that at any football match. Unfortunately it has happened and hopefully we can deal with it in the manner it deserves.”