The Clarets’ four-match unbeaten run was ended by Lancashire rivals Bolton, whose three first-half goals set them on the way to a fourth successive league win.
Burnley included Dean Marney in a three-man midfield as he got another valuable 90 minutes into his legs as he continues to move towards first-team duty.
But his young team-mates found it hard going, particularly in a youthful back four before the break, as Bolton all but secured the points which lifted them above the Clarets in the Professional Development League.
Tinashe Chakwana gave Michael Duff’s side hope as he briefly reduced the arrears to make it 2-1 with his first league goal of the season.
But the visitors were the stronger side and after restoring their two-goal cushion just before the break, wrapped things up with the goal of the game from skipper Liam Edwards eight minutes from the end.
The Clarets were up against it after conceding twice in the opening 10 minutes, despite making a positive start themselves.
A superb pass from Marney almost laid on the opening goal for Khius Metz before Bolton keeper Jake Turner dashed off his line to meet the ball first.
The return of the pacey Metz from injury added to the Clarets’ attacking threat as he offered a willing outlet in tandem with Chakwana and Tunde Bayode.
But it was Bolton who struck first as they caught Burnley cold at the back.
The lively Connor Hall got away down the right to square the ball for strike partner Dennis Politic to drill a shot past Adam Legzdins.
And two minutes later Hall got on the scoresheet himself to make it 2-0 as he stretched to divert home a perfectly delivered free-kick from Harry Brockbank.
Burnley hit back and in a frenetic start reduced the arrears with 20 minutes gone thanks to a high-quality goal.
Former Bolton youngster Jamie Thomas released Marney in behind the Bolton defence and Marney’s low cross was spot-on for Chakwana to sweep the ball home season from six yards.
The Clarets pushed for an equaliser with Rahis Nabi threading through a pass for Bayode, who was well tackled by Edwards as he was about to pull the trigger.
And Metz then shot at Turner after the visitors’ defence had been opened up again.
But the momentum swung back Bolton’s way before the break and they restored their two-goal lead when Jack Earing slipped in Jeff King to side-foot home five minutes before the end of an entertaining first half.
Wanderers were then almost out of sight seven minutes after the re-start when Brockbank was allowed to run un-checked into the penalty area from a free-kick to drill in a shot which the covering James Clarke did well to deflect wide from almost on the line.
Marney did his best to get Burnley back into it with a low drive that was deflected just wide at the other end.
And the Clarets did most of the pressing as they tried to spark a comeback, Thomas almost pulling one back with a free-kick he curled into the side-netting with 10 minutes to go.
But the visitors always had a bit in hand and despite being made to work harder for their openings, made sure of extending their winning run with a superb late strike from Edwards, who collected the ball 30 yards from goal and beat the back-tracking Legzdins with an excellent dipping strike.
It could have been five in stoppage time, but Ali Koiki cleared off the line from substitute Kai Parkinson just as namesake Phil – the Bolton boss – exited his seat after a good night's work from his young hopefuls.
Burnley: Legzdins, Birch, Koiki, Nabi, Younger, Clarke, Thomas, Marney, Bayode, Metz (Wood 69), Chakwana (Limb 74). Substitutes: Stone, Flowers, N’Guessan.
Bolton: Turner, Brockbank, Longsdale, Edwards, Mitchell, Jones, Politic (White 82), Earing (Perry 69), Hall (Parkinson 85), King, Taylor. Substitutes: Aspinall, Moulden.
Referee: John Matthews