Michael Duff’s men well and truly spoiled the Owls’ party with a win that denied Sheffield Wednesday the title and kept the Clarets out of bottom spot.
Wednesday needed only a point to ensure the Professional Development League's northern division tile for the second season in a row.
But two goals in 10 minutes in an excellent Burnley fightback dashed those hopes and prevented the Owls even making the national play-offs as Nottingham Forest pinched second spot on goal difference with a 4-0 lunchtime win at Huddersfield Town.
The home side had a dream start at Hillsborough and took the lead through Preslav Borukov with just three minutes gone.
But goals before half-time from a trialist striker and top scorer Tinashe Chakwana - who later mised an injury-time penalty - saw Burnley take all three points to make sure they will finish above Barnsley at the foot of the table.
Tinashe Chakwana scored his eighth goal of the season
Wednesday started off just the way they would of wanted, Bulgarian U19 international Borukov taking advantage of Oliver Younger’s error at the back to slot home past Conor Mitchell.
The Clarets settled down and began to play some delightful football, finding the net through Chakwana only for hi effort to be ruled out for off-side.
But with quarter-of-an-hour gone Burnley were level, Jordan Cropper whipping in a fine ball for the trialist to pounce and head home.
And 20 minutes later Duff's men had a deserved second, Chakwana poking the ball past Dan Wallis in the Sheffield goal.
Wednesday looked to hit back after the break with Jack Stobbs forcingMitchell into a great save before seeing an effort deflected wide from Younger.
With the Yorkshire side needing only a goal at that stage to take the title they piled the pressure on in the last 20 minutes and almost equalised when Jordan Lonchar headed inches wide of the post.
Five minutes into stoppage time the Clarets were awarded a penalty as Chakwana was brought down by Wallis.
The Wednesday keeper made amends as he saved Chakwana’s spot kick but Burnley had done enough to secure a fourth win in seven games and seven in the last 12 to end their first season at this level on a high.
Burnley: Mitchell, Cropper, Clarke, Younger, Wilson, Koiki, Benson, Goodridge (Perkins 88), N’Guessan, Chakwana, Trialist (Massanka 78). Subs: King.