Jay Donnelly got the only goal of a totally forgettable 90 minutes but it still may not be enough to guarantee the East Belfast team a semi-final date with Ballymena United next month.
It emerged after the game that defender Joe Crowe had still one match of a three-game ban to serve.
The controversy surrounds an Intermediate Cup game involving Glentoran IIs and Lisburn Distillery.
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That fixture couldn’t be used as one of Crowe’s banned games because he was ineligible to play given he had featured 16 times for Glentoran this season – the competition cut-off is 12 games.
It will be now left to Irish Football Association chiefs to sort out, with the Glens now facing possible expulsion.
Although Newry are now clinging to renewed hope of being reinstated to the tournament, manager Darren Mullen believes his boys did enough on Saturday to warrant something from the game.
“This is ultimately where we want to be as a club, competing against the big boys,” claimed Mullen. “We showed what we are about.
“Yes, it took us a while to get to grips with the game in terms of pace, but we were playing against a full-time team, so I have got to praise our lads and their fitness levels.
“We certainly didn’t look out of place against a side that are sitting at the top of the Premiership.
“There was a sense of disappointment in the dressing room after the game because we thought the game was there for the taking.
“We deserved something from the game...we knew how they would play and how difficult it would be, they are a top-class full-time team.
“We had to try and stay with them and match them.
“They moved the ball about well and they moved up well, it was the case of hanging in there.
“They got a little bit of luck with their goal, the guy (Conor McMenamin) got a fortunate ricochet but he still put a great ball into the box and it was a great finish by Donnelly.
“But I thought we were super in the second half.
“When you have a team like Glentoran time-wasting and taking the ball into the corner, you know you have done something right.
“I was gutted for the lads, but I was proud of them.
“You could tell Glentoran were hanging on a bit late in the game.”
On the Crowe controversy, Mullen added: “To be honest, I know nothing about it, I wasn’t aware of it.
“I would have loved to won the game on the pitch, I’m not a big fan of protests.
“I just don’t know what the ins and outs of the accusations are...I’ll leave it to the people at the top (at the IFA) to sort out.
“We wanted to come here and do ourselves justice, we had a belief we could hurt Glentoran because I’ve watched then over the past few weeks.
“I could see areas where we could hurt them – and we did.”
Glentoran boss McDermott had other issues to deal with, namely the Crowe controversy - so he sent coach Kieran Harding to face the media.
“I can’t comment on the situation because we know nothing about it...it has only come to light over the past 10 minutes or so,” said Harding. “Obviously, it’s for the people upstairs (in the Boardroom) to sort out.
“As for the game, we didn’t really get out of the traps.
“Newry came with a gameplan and, to be fair to them, they played well.
“We never got out of second gear, we made poor decisions and were just off it over the 90 minutes.
“We were not our normal selves, no fluidity, no intensity, no passion or appetite.
“The goal was the one bit of quality in the game...it was a great ball in from Conor and a great header at the back post from Jay.
“If anything, we were even worse in the second half, all-in-all, it was poor and ugly.”
GLENTORAN: McCarey, Marshall (Cole, 46), Marron, Crowe, Burns, Murray, Plum (Clucas, 46), McCartan (O’Connor, 71), McDaid (R.Donnelly, 46), J.Donnelly, McMenamin.
Subs (not used): Cushnie, Jenkins, Glendinning
NEWRY CITY: Maguire, King, Healy, Boyle, Hughes, Teelan (Carville, 86), McGovern, Moan, Donnelly (Kelly, 82), Forde (Brennan, 87), Mongomery (Smyth, 86)
Subs (not used): Brady, McKeown, Scullion
REFEREE: Tony Clarke