The young Reds had not tasted defeat in the U18 Premier League all season before the clash at the Academy, which they led at the interval through Glen McAuley.
But Jordan Greenidge levelled the score after the break and Krisztofer Szereto converted a contentious penalty in stoppage-time to snatch three points.
“It was a disappointing result and all the lads are disappointed in the dressing room. We have lost three games on the spin so I will take responsibility for that,” Gerrard told Liverpoolfc.com.
“As far as the game went, I felt we were OK, good enough in terms of the first 45 minutes. At half-time we said to the lads be ready for the battle, be ready for the pressure that comes from Stoke and we were going to need some bottle, some guts, and take responsibility.
“[But] Stoke wanted the result more than us in the second half so that’s the disappointing thing from my point of view.
“Sometimes it becomes more difficult when you take the lead, especially against teams like Stoke. At 1-0 they are never going to go away and they are going to come at you and you have to stand up to that.”
Watch: The best of the action at the Academy
There were some consolations for the U18s boss to take from a tough evening under the floodlights in Kirkby, with McAuley completing 90 minutes as captain and finding the net.
“Glen missed 10 days early in the New Year with a little problem and he has missed a lot of training,” said Gerrard. “But he got his goal, as he does, and it was a positive run-out.”
Meanwhile, U16 graduates Jack Bearne and Niall Brookwell were introduced as substitutes in the second half for their debuts at this level.
“Niall is as honest as the days come. You always know what you are going to get from him and I thought he came on and battled well and tried to use the ball when he got possession,” added the Reds legend.
“Little Jack Bearne, I’ve been impressed with him at U16 level and he’s going to be a player at this level very soon, and he is going to get minutes between now and the end of the season.
“He’s probably not ready for this level just yet but I thought he applied himself really well. He showed some really good touches, good movement and he’s got pace. I hope he enjoyed his debut because I was pleased with him.”