The Clarets’ wait for a Premier League win was cruelly extended after Southampton struck in the last minute in bizarre fashion through the unwitting intervention of referee Bobby Madley.
Ashley Barnes’ close-range header mid-way through the second half looked as though it had finally ended an 11-game winless run.
Barnes had struck the winner that last time Sean Dyche’s side had tasted victory – a late strike against Stoke City lifting Burnley into the top four.
His latest effort was enough to regain seventh place in the table but felt like scant reward after Madley inadvertently played a huge part in Southampton’s last-minute equaliser.
Madley blocked off Burnley midfielder Ashley Westwood and handed possession back to the Saints, who pounced to level through substitute Manolo Gabbiadini and leave the Clarets rueing their collective bad luck.
In a bid to end the winless run, Dyche made changes both to personnel and formation with Westwood returning in place of Sam Vokes in a switch back to a 4-4-1-1 and Jeff Hendrick resuming his more attacking midfield role.
That meant a first home start in the Premier League this season for Westwood, while Stephen Ward also returned at left-back to start his first game since mid-December.
Since then the Clarets had failed to pick up maximum points but, having held champions-elect Manchester City in their previous Turf Moor outing were looking to kick on against a Southampton side struggling to escape the relegation places.
The Saints had won just once in the league since November but were unbeaten in their last three away games and also reached the FA Cup quarter-finals with a win at West Bromwich Albion last time out.
And Mauricio Pellegrini’s side showed no shortage of confidence in a tight first half which brought arguably the best chance for the visitors, Nathan Redmond teeing up Dusan Tadic for a shot which was superbly blocked by Ben Mee as the defender and Nick Pope moved to snuff out the danger.
Watching England manager Gareth Southgate will have taken note, while at the other end it was a former England man Aaron Lennon who went closest to giving the Clarets the lead.
A free-kick from Matt Lowton was headed out as far as the winger whose volley was well struck but, fortunately for Alex McCarthy, close enough for the Saints’ keeper to save as the ball flew through a crowd of bodies.
Lennon had another shot blocked after Barnes had laid the ball off following Lowton's good work, while Johann Berg Gudmundsson headed wide early on from a Ward cross and Hendrick couldn’t make the most of another opportunity created by Barnes as Burnley battled to get their noses in front before half-time.
Then after Southampton had started the second half in positive fashion the Clarets turned up the pressure with Gudmundsson playing a peach of a pass towards Hendrick which the Irishman just couldn’t turn goalwards and Barnes nodding a Westwood cross wide.
But the next time Hendrick and Barnes were involved looked likely to be the pivotal moment as Burnley went in front in the 67th-minute.
There was a growing sense a goal was coming and again it arrived as the Clarets attacked the Jimmy McIlroy Stand.
Gudmundsson’s late strike at that end had secured the point against City and he almost scored again when he met an excellent cross from Lennon on the volley beyond the far post.
McCarthy did well to palm the ball out, but Hendrick nodded it back for Barnes to throw himself full length and head in from a couple of yards to claim his fifth goal of the season – joining Chris Wood as leading scorer.
Pellegrino reacted by sending on Josh Sims and the young winger made an immediate impact, almost equalising with his first meaningful touch.
Southampton had barely threatened in the second half but a slick counter-attack gave Sims the chance to shoot and it took a superb finger-tip save from Pope, touching the ball onto the outside of the post, to preserve the Clarets’ lead.
Burnley looked like they had done enough to secure a third successive 1-0 win over the Saints but as they closed in on an 11th clean sheet of the campaign Southampton struck in the last minute to deny Dyche's men their overdue victory.
And the goal was doubly painful after Madley inadvertently played a huge part.
Madley blocked the impressive Westwood from tidying up in midfield and with the visitors gifted the ball they took full advantage.
Sims’ cross was nodded down at the back post by Guido Carrillo for Gabbiadini to swivel and volley in the goal that aided the Saints’ survival hopes and extended the Clarets’ frustrating wait for all three points.
Burnley: Pope, Lowton, Cork, Mee, Barnes, Hendrick, Berg Gudmundsson, Westwood, Ward,Lennon, Long. Substitutes: Lindegaard, Taylor, Nkoudou, Marney, Vokes, Wood, Bardsley.
Southampton: McCarthy, Soares, Stephens, Hoedt, Carrillo, Tadic (Gabbiadini 81), Romeu (Boufal 75), Ward-Prowse (Sims 68), Lemina, Bertrand, Redmond. Substitutes: Forster, Højbjerg, Pied, Bednarek.
Referee: Bobby Madley