The Magpies were back in action after an 18-day hiatus and were nine minutes away from claiming a point that would have moved them out of the bottom three before Xherdan Shaqiri fired in a 25-yard winner in the Potters' 1-0 win.
Even then McClaren's men almost came away with a point when Seydou Doumbia saw a stoppage-time attempt turned away by Jack Butland, who had not been troubled up until that point.
Newcastle have not won on their travels since a trip to Tottenham on December 13 and, while they left Staffordshire empty-handed, McClaren thought they produced an improved showing from their 5-1 loss to Chelsea last time out.
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"We didn't deserve that," McClaren declared.
"Jack Butland has become a bit of a curse this season for us. Four magnificent saves at St James' and one at the end there which denied us a point. That's the difference at the present moment.
"But, the last 18 days, we talked a lot about what we need to do and I think we started that process tonight in terms of attitude, work-rate and becoming harder to beat. I thought we were very organised, very disciplined.
"We stifled, frustrated Stoke - so much so that I think they had one shot in the second half and it's a goal. Treacherous conditions and I thought we deserved to fight our way to at least a point.

"If you had seen the performance at Chelsea compared to this evening...(it's) most definitely (an improvement). I thought there were good individual performances, a good team performance - you could see there was a determination, a work-rate for each other and a spirit there.
"This game's cruel and it's been cruel to us again. Dust yourselves down and we go again on Saturday."
While Newcastle fear spending next season in the Sky Bet Championship, Stoke supporters are dreaming of European football after Shaqiri's strike lifted them up to seventh.
"We're pleased with the three points - it's three wins on the bounce, we're in seventh and we're doing okay," Potters boss Mark Hughes said.
"In terms of wins we're very similar in terms of what we've been able to achieve. There's other clubs who have a hell of a lot more resources than us and we're on a similar level at the moment.
"It's important to get momentum at this time of the year and it seems like we are. We've got a difficult game at the weekend against Chelsea which will test us.
"With the games that we've got left, we're confident that we will get a good total by the end of the year."

The Potters have ended the previous two campaigns strongly too and Hughes does not expect them to stumble down the stretch this time.
"We're hoping that's going to happen again," the Welshman said of finishing with a flourish.
"There's no guarantee of it but the way we work, the way we train and the standards that we like to keep right throughout the year, that sustains us. We don't allow their energy to drop or their focus, that's helped us every year I've been here, so we fully expect that to happen again."
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