Boss Tony Philliskirk praised the Clarets' fighting spirit after they came from behind to take a point from the league leaders.
Michael Fowler fired Burnley head in Philliskirk's first game fully in charge of the Under-18s.
And after the Owls had struck twice, the skipper then doubled his tally with a last-gasp penalty to level things up after defender Richard Taylor had been stretchered off following a blow to the face.
Philliskirk said: “I thought Sheffield Wednesday were the better team in the first half. They’re top of the league for a reason and you could see why.
“But in the second half you could see us growing into the game.
Michael Fowler is the Clarets' leading scorer
“Will Harris hit a post and their goalkeeper has made a good save. There were a couple of scrambles and you begin to think ‘is it going to be one of those days?’.
“Then, unfortunately, Richard Taylor went in bravely and headed the ball goalwards and got kicked in the face and was knocked out.
“The referee awarded the penalty but the most important thing at that time was Richard’s well-being, so it took time to see to that.
“Michael had a really long wait to take the penalty and showed great composure to stick the penalty away and then there about eight minutes left to play after that and we looked like we could grab another.
“We were in the ascendency and that says a lot for the spirit and the determination of the lads.
“No matter what you say, technically and tactically, if you’ve got that you’ve got something to work with, so I was very pleased for the lads.”
Burnley: Calderbank-Park, Moss, Rain, Woods (Yari 71), Taylor (Patterson 90), Pruit, Meredith, Kershaw, Fowler, Harris, Steels (Smith 68) Subs: Allen, Mupariwa.