The Magpies boss is remaining confident that his side will survival despite failing to see out a point at the Britannia Stadium.
The Magpies conceded an 81st-minute winner at the Britannia Stadium when Xherdan Shaqiri's shot from 20 yards flew past Rob Elliot, before being denied a point by a stunning save from otherwise-untested Jack Butland in injury time.
The defeat saw McClaren's side miss the opportunity to lift themselves back out of the relegation zone by avoiding defeat in their game in hand, and leaves them second-bottom of the table on goal difference.
The former England manager said that the defeat was a cruel one, bemoaning Butland's heroics, but remained adamant that his side will still stay up.
He told BBC Sport: "I’m glad we don’t have to play against Jack Butland every week. He denied us victory at St James’ Park and tonight he denied us a point I think we deserved. It’s cruel that we lost.
"It’s difficult to stomach but you have to. I couldn’t fault the players. We were organised, hard to beat, compact and we frustrated Stoke, they had one shot in the second half and scored.
"If we continue that hard work then we will get what we deserve. Saturday at home against Bournemouth is a big game, we've got 11 games left and need a certain amount of victories. With the talent we have got, we’re confident to we can do it."
Wednesday's defeat was Newcastle's seventh in a row away from home, and McClaren and his players will be relieved to be heading back to their own fans at the weekend.
The Magpies next two home matches are crucial to their survival bid as they face 15th-place Bournemouth on Saturday before a pivotal Tyne-Wear derby against Sunderland on 20 March.