The Clarets were unable to shake off their Millwall jinx as the Lions struck late to take a point on an incident-packed afternoon at Turf Moor.
Charlie Austin’s 11th goal of the season and a career first from Ben Mee looked as though they had given Burnley a third home win of the season after recovering from Liam Trotter’s early strike.
But a controversial decision to disallow a second-half Junior Stanislas ‘goal’ for what was almost a retrospective off-side decision kept the Lions in the hunt.
And in injury time Darius Henderson preserved an unbeaten record in Burnley stretching back seven years when he pounced to equalise in a dramatic finish.
Burnley boss Eddie Howe had wanted to revert to the side which had won at Derby a week ago, but whereas captain Jason Shackell had come through the warm-up at Pride Park unscathed this time he pulled up with the return of an injury problem to the back of a knee.
That meant a rapid recall for David Edgar but the defence that had served the Clarets for most of last season was breached after just three minutes as Millwall went ahead.
The Lions gave instant notice of their threat on the break as Trotter broke from midfield before exchanging passes with Andy Koegh and sweeping a shot beyond Lee Grant, who probably should have done better.
For a team which had won its last two games at Turf Moor it was the perfect start as the Londoners sought to end a three-game losing run.
Burnley’s seemingly fragile confidence may have taken a blow but to their credit the Clarets mounted an instant response and could well have been level before Mee did peg the visitors back.
Man mountain Danny Shittu just won a race with Martin Paterson to clear from virtually off the line after goalkeeper David Forde had failed to deal with a long ball from Edgar before the Irish international made amends by beating away a fierce drive from McCann.
Stanislas then missed a decent chance at the near post after Paterson had pulled the ball back before Stanislas delivered the corner which Mee met with a perfectly timed run to head powerfully past Forde.
With only one clean sheet between the two sides this season that always looked unlikely to be that and the Clarets were adamant they should have had penalties when Shittu appeared to block a goalbound Patterson effort with his outstretched arms and defender Alan Dunne punched away a cross.
Stanislas, always a threat from set-pieces, then curled a long-range free-kick inches over the bar but Millwall remained positive themselves and Grant twice needed to redeem himself for his earlier error by touching a thumping volley from Scott Malone onto the bar and then going full length to keep out a James Henry effort.
Perhaps the only surprise was that none of the catalogue chances had come Austin’s way but that all changed two minutes before half-time when the country’s leading marksman got his customary goal.
And as ever he needed only one sight of goal to make it count, finding space to meet a ball forward from Kieran Trippier at the end of a well crafted move with a beautifully directed header from all of 15 yards which arced perfectly into the top corner.
But if Burnley had hoped that would deflate the Lions it didn’t prove to be the case as they started the second half intent on hunting down an equaliser.
The Clarets needed to stand firm and weather a bout of pressure which they did with some committed defending, epitomised by McCann’s headed clearance from a dangerous Malone free-kick.
And their resolution looked as though it had paid off when Howe’s men thought they had added a third with 63 minutes gone before a remarkable, and almost unprecedented, intervention from the officials.
With no flag raised, Stanislas accepted a return pass from Paterson to run clear and bury a low shot past Forde to seemingly safeguard the points.
But following complaints from the Millwall players, referee Craig Pawson consulted with assistant William Smallwood who must have belatedly decided that Paterson had been standing in an off-side position and with the ball back on the centre spot raised his flag to rule out the ‘goal’.
The decision may ultimately have been the right one but the way it was handled did no favours for the referee, who then struggled to re-assert any sort of grip on the game which headed for a fractious finish as four more players received yellow cards.
It became a test of concentration for the Clarets and one they looked to have passed until Millwall levelled two minutes into stoppage time.
Stanislas had blasted a shot over at the other end and Edgar saw an effort cleared off the line by Jack Smith as time began to run out.
But with five minutes added there was still scope for a final twist to a remarkable afternoon.
A header from Woods that hit the bar looked like Millwall’s last chance of a point but still they kept going and after Henderson had controlled a ball over the top and steered a left-foot shot past Grant to make it 2-2, the substitute then almost forced a winner when his effort deflected off Mee, hit the underside of the bar and bounced down on the line.
Burnley: Grant, Trippier, Mee, Duff, Edgar, Marney, McCann (Bartley 71), Wallace (Stewart 90), Austin, Paterson Vokes 75), Stanislas. Subs: Stock, Mills, Long, Jensen.
Booked: Marney 35, Mee 56, Wallace 70, Vokes 81
Millwall: Forde, Dunne, Shittu, Robinson (Smith ht), Lowry, Malone (Batt 67), Trotter, Henry, Keogh (Henderson 64) , Abdu, Wood. Subs: Wright, Henderson, Racon, Mkandawire, Taylor.
Booked: Trotter 32, Dunne 57, Henry 72, Lowry 79
Referee: Craig Pawson