A superb second-half fightback saw the Clarets score four times to secure the win which took them up to second spot in the Professional Development League’s northern group.
Trailing 2-0 at the break, Burnley’s three-game unbeaten run was in danger of coming to an end.
But Steve Stone’s youngsters raised their game to dominate the second half at Leyland’s County Ground and complete the double over their Lancashire rivals.
Three days after drawing with Liverpool to enhance their chances of progressing in the Premier League Cup, the Clarets made a handful of changes as midfielder Christian N’Guessan and defender Teddy Perkins both returned from long-term injury.
There was also a first starting chance for youth-team striker Michael Fowler (above).
And it was his goal with an hour gone which sparked the fightback.
Fellow second-year scholar Bobby Thomas then headed the equaliser two minutes later.
Josh Benson had a hand in all four goals
And the comeback was completed as substitute Dan Agyei headed Burnley in front before dead-ball expert Josh Benson curled in the fourth two minutes from the end.
The Clarets could have lead inside the opening couple of minutes as captain Anthony Glennon thundered an effort off the bar from a Benson corner.
Glennon, operating at left-back to accommodate the return of Perkins at centre-back for the first time since September, delivered a stream of excellent crosses before the break.
But no-one in a black shirt was able to get on the end of them and the Clarets allowed Bolton a soft lead from two defensive lapses.
Thomas was caught out in the first as Olowale Tanimowo was allowed to stroke Bolton in front.
And the Wanderers front-man doubled his side’s advantage six minutes before the break after Benson had been caught in possession.
Aiden Stone also needed to save from Bolton captain Harry Brockbank, but Bolton never threatened again once the Clarets took a grip after the break.
Fowler showed his predatory instincts to help the ball over the line from a Thomas header to make it 2-1.
And Bolton were unable to cope with the Clarets’ set-plays and the introduction of Agyei from the bench.
Thomas neatly guided in a header from another Benson corner to level the scores.
And after Agyei had been denied by Bolton keeper Jake Turner, he got the goal he deserved when powering home a header from a pin-point Benson free-kick.
The midfielder’s delivery had been impeccable and Benson got himself on the score sheet just before the end with a wonderful curling free-kick to cap another fine night’s work from Stone’s in-form side.
Bolton: Turner, Brockbank, Johnson, Zouma, Hartshorne, Earing, Doyle (Boon 62), Jones-Griffiths, Tanimowo, Duke-McKenzie (Navarro 73), Darcy. Substitutes: White, Aspinall, Brown.
Burnley: Stone, Cropper, Thomas, Perkins, Glennon, Bayode, Benson, N’Guessan, Blair (Chakwana 64), Fowler, Harker (Agyei 60). Substitutes: Calderbank-Park, Clarke, Yari.
Referee: Dean Watson