Craig Davies and David Ngog came off the bench to turn a Lancashire derby on its head and hand Bolton three much-needed points.
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Following a goalless first-half of few chances, Burnley looked set to claim local bragging rights from the second time this season following David Edgar's close-range finish in the 55th minute.
It prompted Wanderers boss Dougie Freedman to introduce strike pairing Davies and Ngog, initially to howls of derision from the Reebok Stadium faithful who were unhappy to see Marvin Sordell and lively winger Steve De Ridder withdrawn.
But the switch proved to be inspired as Davies headed his first goal since joining from Barnsley last month before Ngog sealed the Trotters' maiden league triumph of 2013 nine minutes from time.
Freedman's men climb to 16th in the npower Championship table, although they remain three points above the relegation zone.
Burnley slip behind bitter rivals Blackburn into eighth, four points shy of the play-offs.
On-loan West Brom centre-back Craig Dawson made his Bolton debut at the expense of Tim Ream, while deadline day signing De Ridder was handed a first start.
Edgar replaced injured defender Michael Duff in Burnley's only change.
The visitors made an enterprising start and Bolton had Darren Pratley to thank for keeping the game goalless in the 17th minute.
Ross Wallace - fresh from signing a contract extension at Burnley this week - collected Dean Marney's return backheel from a cleverly-worked short corner to drive across the face of goal, but Wales international Pratley hacked clear.
The deadlock should have been broken from a corner at the other end mid-way through the half when Dawson was left unmarked to head Jay Spearing's outswinger narrowly wide at the back post.
De Ridder was proving to be one of Bolton's more potent attack threats on the right flank and he burst past Clarets midfielder Chris McCann to have an angled 29th minute effort deflected past the far post.
From the resulting corner Dawson was again the man to connect and brought the half's only meaningful save from Lee Grant.
Eagles drove at the Burnley defence and speculatively shot wide from 20 yards before Pratley saw a strike from further afield deflected behind.
Once more, Dawson was off-target from the set piece that followed as Bolton ended the half in the ascendancy.
Given the predominant method of creating chances in the match, it was somewhat inevitable when Burnley went ahead from a 55th minute corner.
Wallace hung up a cross to the back post where McCann towered above the Bolton defence to nod back across goal and leave Edgar with a simple nodded finish.
Then came Freedman's ill-received changes that would send a sceptical Reebok crowd into raptures.
In the 66th minute, Lee Chung-Yong engineered room to swing a ball in from the left and Davies glanced beyond Grant via the underside of the crossbar.
Grant was forced off his line to thwart Davies when a slick one-two with Ngog split the Burnley defence but the Clarets goalkeeper had cause to be less happy with his work in the 73rd minute, fumbling a Spearing set piece that resulted in Dawson and Marcos Alonso having goalbound efforts hacked clear.
Alonso brought a superb save from Grant with a venomous 30-yard free-kick that was turned behind and from the subsequent corner Wanderers' pressure told.
As another substitute, Kevin Davies, made a customary nuisance of himself Burnley were unable to fully clear. Spearing drove back towards goal where Ngog stole in front of Burnley full-back Danny Lafferty to turn the ball home.