The Clarets suffered a fifth successive defeat in the U23 Professional Development League but didn’t go down without a fight against the northern group leaders.
Bolton have proved almost unstoppable in recent months and have now lost just one of their last 14 games.
Burnley's Lancashire rivals started with former Bayern Munich midfielder Jon Kirchhoff in their line-up as the ex-Sunderland man looks to earn a contract at the Macron Stadium.
Jan Kirchhoff was capped 18 times by Germany under-21s
And on-loan Liverpool defender Jon Flanagan – who spent last season as a Claret - also got a start as the Trotters went for an 11th win of their recent impressive run.
Burnley’s form has been a polar opposite with Michael Duff’s ever-changing side currently propping up the table after conceding eight goals in their previous two league games as they look to find their feet at this level.
But another inexperienced team showed great character and desire to push Bolton all the way with only a late goal from substitute Chinedu Obasi denying the Clarets a morale-boosting point ahead of next Monday’s pivotal Premier League Cup tie against Swansea City.
Jon Flanagan made 10 appearances on loan for Burnley last season
When Bolton had won the reverse fixture in November to launch Burnley’s losing league run they had been virtually out of sight by half-time as they built up a 3-1 lead.
But this time the Clarets showed greater resolve to keep the leaders at bay in a highly competitive derby.
Eighteen-year-old centre-back Scott Wilson was excellent in a resolute back four effectively shielded by deep-lying midfielder Christian N’Guessan.
But it still needed a fine performance from goalkeeper Conor Mitchell to keep the score goalless at the break as the Northern Ireland under-21 international made a handful of smart saves.
His first came 10 minutes in as he beat away a shot from eye-catching left-back Joe Muscatt and in stoppage-time at the end of the opening half he denied the same player again with his legs.
In between there were stops from Liam Morris and Connor Hall but there were also spells of respite as the Clarets looked to strike on the counter-attack.
Two free-kick opportunities gave Jamie Thomas and Rahis Nabi the chance to try their luck from distance, but neither were able to find a way past Jake Turner.
Bolton threatened again at the start of the second half with trialist Frank Jones having to nod a Hall header off the line and Mitchell going full length to keep out the resulting corner from Morris at his near post.
But the home side withdrew Kirchhoff and Flanagan after an hour and the Clarets went on to have their best spell as they sensed a possible opening goal.
Ntumba Massanka had seen an effort deflected wide and Burnley, with Tinashe Chakwana introduced from the bench to try and add a cutting edge, pressed Bolton back in a sustained spell of pressure.
Chakwana tested Turner with a low drive but with eight minutes to go it was Bolton who grabbed the winner when Obasi avoided a couple of challenges as he cut into the penalty area following a throw-in to strike a low shot into the bottom corner and deny battling Burnley the chance to stop the rot.
Even then Duff’s men launched a late rally to try and earn some reward but Bolton survived six minutes of added time with 10 men following an injury to Hall as they greeted the final whistle with some relief to keep their title challenge on course.
Burnley: Mitchell, Birch, Jones, Wilson, Koiki, N’Guessan, Bayode (Barnett 81), Nabi, Thomas (Chakwana 65), Jackson (Wood 85), Massanka. Substitutes: Stone, Glennon.
Bolton: Turner, Flanagan (Obasi 60mins), Muscatt, Edwards, Mitchell (Rose 70), Brockbank, Morris, Kirchhoff (White 60mins), Hall, Charsley, Earing. Substitutes: Rose, Aspinall, White, Obasi, Jones-Griffiths.
Referee: Paul Brown