Wanderers exited the Carling Cup at the third round stage as they were edged out by a single goal at Burnley.
A dubious goal from Wade Elliott a minute before half-time was the only difference in a typically paced cup tie at Turf Moor.
Referee Mark Clattenburg needed to consult his assistant referee as to whether the ball crossed the line before making the decision in the home side's favour on 44 minutes.
Wanderers will consider themselves unfortunate to be out of the competition as they conjured up several opportunities in both halves.
Debutant Rodrigo, Ivan Klasnic, Tamir Cohen and Matt Taylor all brought superb saves out of Burnley goalkeeper Lee Grant.
But there was no luck in the final third for Owen Coyle and his team on the manager's return to his former club.
As anticipated, there was a loud and passionate atmosphere leading up to kick-off, particularly when both teams emerged from the tunnel.
The noise created by the two sets of supporters set the tone for an end-to-end first-half.
It was Brian Laws' men who enjoyed the brighter start as Chris Eagles twice came close to giving the hosts the lead inside the first three minutes.
After bringing Adam Bogdan into action within the first 60 seconds with a snap-shot from a tight angle, the former Manchester United man was to go even closer with a drive from all of 25 yards.
Eagles cut inside from the right and hit a venomous shot with his left foot that struck the frame of the goal, leaving the Wanderers goalkeeper helpless.
In the Clarets next attack, Eagles was once again at the centre of the action, but this time he was the provider, delivering a curling cross which Chris Iwelumo could only prod towards Bogdan.
The pace of the tie in the opening exchanges was electric, and after absorbing the early pressure inside the first ten minutes, Bolton began to get a grasp of the game.
Rodrigo Moreno, one of eight changes to the team from the side that played Aston Villa, gave the travelling fans an early sight of his pace and tricky in Wanderers' first real attack of the game.
Former home favourite Robbie Blake played a sweeping ball out to the right, and after beating left-back Danny Fox, the on loan Benfica forward curled an effort goalwards which was well held by Lee Grant.
Six minutes later and the former Sheffield Wednesday stopper made an even better save to prevent Tamir Cohen from scoring in his first match of the season.
Again it stemmed from another slick Wanderers attack as Ivan Klasnic laid the ball into the Israeli midfielder, who drilled in a fierce effort from outside of the box which was destined for the far corner, up until Grant's heroics.
The visitors were now in the ascendancy and Burnley were finding it particularly difficult to cope with the threat of Rodrigo, who seemed to have the beating of Fox every time he picked up possession of the ball on the right wing.
Before the half was out, there was still time the number 19 to again terrorise the Clarets' defence with a mazy run, while Blake also took on the home defence before bringing a competent save out of Grant.
However, Burnley rallied in the final five minutes of the half and they broke the deadlock on the stroke of half-time, albeit in controversial fashion.
Moments after Jay Rodriguez struck the crossbar with a shot from distance, Wade Elliott was well positioned inside the area to covert Eagles cross from the byline.
Bogdan made the save but after consulting his assistant referee, Clattenburg awarded the goal, deeming that it crossed the goal-line.
The official had origininally signalled for a penalty after the ball struck a stray hand inside the box, however he over turned that decision to give Burnley the lead.
The opening minutes of the second-half passed by without much penalty area action, but Wanderers came to life on the hour mark, carving through Burnley's defence twice in quick succession as they sought the equalising goal.
Firstly Ivan Klasnic beat the offside trap to test Grant with a thunderous left-foot effort and then in the next attack Cohen skewed a shot wide of the near post having seemingly done all the hard work.
Again a pass from midfield evaded the Clarets' rearguard, and after turning past Clark Carlisle, the number 21 dragged his attempt wide of the near post from eight yards with Grant beaten.
Wanderers boss Owen Coyle opted to shake things up with 20 minutes left as he made his first changes of the game.
Rodrigo, who had enjoyed a lively debut, was brought off along with Klasnic. Johan Elmander and Chung-Yong Lee were the two attackers introduced.
Matt Taylor saw two free-kicks drift wide of the post, Cohen headed narrowly wide from a corner as Wanderers dominated proceedings until the very end.
Indeed with the last opportunity of the game, Grant pulled off another excellent save to thwart yet another set-piece from Taylor.
In the end, there was to be no way past Burnley's resolute defence, meaning that Wanderers' cup commitments are put on hold until they enter the FA Cup at the third round stage in January.
Burnley: Grant, Alexander, Fox, Carlisle, Cork, Iwelumo (Thompson 73), Elliott, Mears, Bikey, Rodriguez (Marney 88), Eagles (Paterson 82) (Subs not used: Duff, Cort, Easton, Jensen)
Wanderers: Bogdan, Steinsson, Knight, Ricketts, Alonso, Rodrigo (Chung-Yong Lee), Cohen, Mark Davies, Taylor, Blake, Klasnic (Elmander 71) (Subs not used: Lainton, Robinson, Muamba, Holden, Petrov)