The Black Cats took the lead through a fine Josh Hawkes finish and an Aiden O'Brien penalty, but a Jamie Proctor goal made it a nervy finish at Vale Park.
Johnson had made eight changes from the side that beat Wigan Athletic on the opening day of the campaign, and felt that lack of familiarity played its part in the contest.
But with a number of young players impressing, including Ellis Taylor on full debut in an unfamiliar full back role, Johnson said it was a good night for the club.
"It was a really good learning experience for us," Johnson said.
Newcastle United consider loan for £58m 'captain' as Chelsea trio remain on Eddie Howe's radar
Goncalo Ramos' 14-word response to Newcastle United transfer interest following ‘bid’ reports
New £26m signing that Newcastle United bid for suffers major injury blow against Everton
Newcastle United have £17million offer for Watford star rejected - reports
Newcastle United 'closing in' on £13m striker following St James's Park visit
"I wasn't too vocal on the sidelines because I wanted the young lads to try and solve the problems, the seniors to help them solve it.
"I thought we coped, at times we should have had more spells than we did. I think that's a little bit to their quality, and a little bit probably due to a lack of cohesion on our part. That XI probably hasn't had the same level of work as the lads who started against Wigan.
"What you would say is a lot of those young lads stepped up in front of a proper crowd.
"That's what you try and focus on. You want to win the game, get in the hat, and also a club come out of it in a stronger position.
"I thought we did that, by winning against a really senior Port Vale side where we've learned a lot.
"We could have been a bit more confident at times, especially in the first half where we probably had five or six unforced errors in good positions,
"Part of that I thought was down to quite a sticky pitch, and they're a well-versed League Two side, with a lot of experience.
We had to cope, and generally we did. Obviously we've given a poor goal away and that made it a proper cup tie, but we coped."
Johnson also praised Hawkes for his contribution.
The 22-year-old saw his progress checked by a positive COVID test early in pre-season, but is now back up to full speed as he pushes for more gametime.
"I thought he came back flying," Johnson said.
"We asked him to put the work in ahead of pre-season and he did, and in those first couple of weeks he looked really strong, really fit.
"He was really unfortunate in getting COVID, which definitely knocked him back four or five weeks.
"What I want from Josh is that last fifteen minutes of the first half more often, he's so dangerous when he gets in those positions, he can really deliver with a bit of violence and venom.
"He can come inside and strike it, go outside.
"That first goal is a great one from a team perspective and it's obviously a great finish from Josh."
Johnson said the club was still very much active in the transfer market, with Tottenham Hotspur youngster Dennis Cirkin said to be closing in on a move.
"We're still very much looking," Johnson said.
"I've obviously missed today in with preparation for the game, but we're ever hopeful."