The Clarets' bid to make it a hat-trick of Championship wins never made it out of first gear as bogey team Reading left it late to snatch the points at Turf Moor.
Burnley were a pale shadow of the side that had built up a head of steam before the international break.
And even the consolation of a point and a second successive clean sheet was taken away from them in the 99th-minute when substitute Jem Karacan pounced in dramatic fashion to condemn the Clarets to a second home defeat of the season.
Given a lengthy bout of extra time due to a prolonged injury stoppage when Jay Tabb was knocked unconscious, the Royals made it eight wins from their last 11 meetings with Burnley - helping erase further the memory of their 2009 play-off semi-final defeat.
And it was hard to argue they didn't deserve to shade a poor game, leaving the Clarets to lift themselves for next Tuesday night's trip to Barnsley to get their up-and-down campaign back on track.
Having named the same starting line-up for a fourth successive game, Howe saw his side make a bright start in their bid pick up where they had left off before the two-week shut-down.
Eddie Howe tries to lift his troops
Jay Rodriguez went close with an angle shot which flew across the face of goal with a deflection taking the ball away from strike partner Charlie Austin as he waited to pounce.
And Ross Wallace thundered a left foot shot over the top as he ran into a throw-in from Kieran Trippier.
But despite the continued promise of the Wallace-Trippier partnership down the right side of the Clarets' attack and the hard work of Rodriguez and Austin, Burnley's early momentum gradually petered out as Reading grew in confidence.
The Royals, on the back of their own four-match unbeaten run, were the first team to win at Turf Moor last season and almost went in front again after 27 minutes.
Former Reading defender Andre Amougou was unable to cut out a long ball from Kaspars Gorkss, allowing Adam Le Fondre to get in behind the Clarets' defence.
The angle was against the striker but Lee Grant still needed to make a sharp save at his near post as Le Fondre went for goal.
Charlie Austin mounts a rare threat
The former Rotherham marksman then had the ball in the net moments later after Grant parried out a cross from Jobi McAnuff, only to see his celebrations were cut short by the assistant referee's flag.
And having negotiated a tricky 15-minute spell, Burnley almost took the lead in first-half stoppage time as Wallace's deflected shot was only just scrambled away by Adam Federici as the ball threatened to loop under the crossbar.
It was far from convincing stuff, though, and Howe waited just nine minutes into the second half to make his first change as Keith Treacy came on for Junior Stanislas to try and inject some menace into the Clarets' attack.
Two minutes later Burnley created their best chance, although it came via the combination of Reading old boys Austin and Marvin Bartley.
Bartley's powerful run from midfield had the Royals on the retreat and after playing a one-two with Austin, the powerhouse midfielder was denied his first Burnley goal only by Federici's block at the foot of a post.
Jay Tabb is flat out as he waits for treatment
Reading still posed a sporadic threat on the break, Simon Church heading a Joseph Mills corner, but the visitors lost influential midfielder Tabb mid-way through the half when the little midfielder was felled by a clearance from Grant.
Apparently knocked out by the force of the ball, Tabb required more than five minutes of treatment before being stretchered off to be replaced by Karacan.
Reading still sensed a possible winner, though, and substitute Noel Hunt was not far away from providing it as he steered a header just wide from Hal Robson-Kanu's driven cross before Mathieu Manset curled an effort even closer with his first touch after coming off the bench.
The Clarets were getting increasingly anxious and with 83 minutes gone were handed a major a let-off as Le Fondre broke away and after knocking the ball past Amougou went to ground under a challenge from the Burnley defender.
Reading were adamant they should have had a penalty, while Amougou's exaggerated claim that Le Fondre had dived earned him a booking from referee Phil Gibbs, who then added nine minutes of stoppage time.
Reading pounce to win it late on
Even that didn't look enough to produce a goal until 30 seconds from the end when Reading struck to take the points south, Karacan stabbing the ball home at the far post after Hunt's low cross had found a route across goal.
Burnley: Grant, Trippier, Easton, Edgar, Amougou, Bartley, McCann, Wallace, Rodriguez, Austin, Stanislas (Treacy 54). Substitutes: Mee, Marney, Hines, Stewart.
Booked: Trippier 36, Amougou 85
Reading: Federici, Cummings, Pearce, Gorkss, Mills, Tabb (Karacan 73), Leigertwood, McManuff (Hunt ht), Church (Manset 81), Le Fondre, Robson-Kanu. Substitutes: Harte, McCarthy.
Booked: Mills 87
Referee: Philip Gibbs.
Dejection for Burnley defender Kieran Trippier