However, a stream of substitutions disrupted the home side's rhythm and Andras Rado reduced the deficit with a penalty in the 67th minute before grabbing a second with three minutes remaining.
Sean Kelly, Craig Slater, Jack Grimmer, Joe Chalmers, Sam Stanton, John McGinn and Danny Handling all made their debuts at various stages of the game and coach Stark insists they have given him "food for thought" for the visit of the Dutch.
With three games remaining in Group 3, the young Scots sit fourth after five games, six points adrift of leaders Slovakia - who have played a game more - and three behind the unbeaten Netherlands, who have played a match less.
"Hungary had the upper hand in the second half, there is no doubt about that, they played a really good counter-attacking game which I think will stand us in good stead for Holland who look to break quickly," said Stark.
"So the purpose of the exercise was fulfilled. We would have loved to have won the game but a newish group of players within that group gave us some food for thought, definitely.
"We had to look at getting players game time. I think the team that finished the game, apart from Callum McGregor, would be available for the next campaign so it was a young side and I think it showed. The game management side wasn't great for us.
"We didn't have Ryan Jack and Andy Robertson who are our usual full-backs, and quite important to us, and we made changes on top of that so I am delighted to get a number of players game time.
"There were a lot of debutants on the one night so you could argue that it is not that surprising that we didn't quite get going in the second-half.
"Against that, the quality of opposition was decent and we had a new system and it contributed to us losing the lead that we had but we will concentrate on the good performances.
"We would have maybe have taken a draw before the game but I have to be honest, after playing well and getting into a winning position, it is disappointing, there is no doubt about that."
- Sports & Recreation
- Jack Grimmer