The young Magpies trailed inside eight minutes of their opening Northern Section Group C encounter following Joe Felix's strike before Vakhtang Salia's clinical finish drew the hosts level on the stroke of half-time at the LNER Community Stadium.
Kyran Thompson, making his first Magpies start at Under-21 level, fired Newcastle's youngsters ahead within the opening minute of the restart before Afner Cá's late effort sealed maximum points as well as a first win of the 2026/27 season.
Stockdale told newcastleunited.com: "We're really pleased with the result. We had to weather the storm for the first 20-25 minutes and I was a little bit disappointed with our one-versus-one duels.
"I felt we were a little timid in them, having the goalkeeper (Roman Dowell) to thank that the score was only one-nil after making some top saves.
"We then grew into it, got a bit of control and the game changed after scoring right at the end of the first half. In the second half, I thought we were worthy of the result, creating the better chances and we stuck to our shape, staying disciplined.
"I thought we got we deserved in the end against a really good team."
Stockdale was pleased for Thompson and Cá to get off the mark since their respective summer moves from Arsenal and Levante, and is hopeful a number of teenagers can also seize their opportunities at Under-21 level this term.
Newcastle's youngsters aim to qualify for the EFL Trophy knockout stages for the first time since 2018/19 and, with Bradford City and Rotherham United still to face in their respective group, the Redcar-born coach believes the competition will provide "brilliant" experiences for his youthful group.
"(Kyran's) a really good player," Stockdale explained. "It's not easy for anybody to come into a new club and team. We lost some players on loan, others are in the first team squad which is brilliant and it's the next group that come through that need to grasp their opportunity.
"Afner's a different kind of profile player to what we've had in the past. It's not easy for a young player that doesn't speak a lot of English to come into our programme. There's a lot of work to be done with Afner but the raw tools, being quick and strong, are there.
"We were really young at one stage tonight and that's great experience for those players. They'll have dips, moments where it doesn't look great for them and we have to support them when that happens but we demand and push them as much as we can.
"For me, the EFL Trophy and National League Cup are great games for our learning."
Despite a challenging start in all competitions, Stockdale believes the schedule has proved highly positive for United's second-string in the opening stages of the season.
Newcastle's youngsters return to Premier League 2 action on Saturday, facing their Leeds United counterparts at the LNER Community Stadium (kick-off 12:30pm BST) before taking on League One Bradford City on Tuesday 22 September (kick-off 7:30pm BST) and Stockdale believes the quick turnaround in fixtures can benefit his developing squad.
He added: "There's been a couple of performances we haven't been happy with but, results aside, I actually thought the first block of games was really good for us.
"It felt like what the senior team would do. We play Tuesday, Saturday and Tuesday this week and if our players go out on loan or play for the first team, they'll be expected to perform in those games.
"I've really enjoyed our first part of the season. We certainly let ourselves down in the Fulham game but tonight was gritty and there was good football on show, much more what we expect from a Newcastle United team."
