The Clarets extended their unbeaten run to six Premier League games with an injury-time equaliser on an afternoon of penalty drama at Turf Moor.
It looked as though Southampton would leave with a vital three points in the battle just above the bottom three after the Clarets were controversially denied a first-half spot-kick and Nathan Redmond put the visitors ahead 11 minutes after the break.
To add insult to injury Ashley Barnes was booked for diving for the incident which saw him floored by Saints’ keeper Alex McCarthy.
But in stoppage-time the Clarets were finally awarded a first penalty in 68 Premier League games when defender Jack Stephens blocked a header from Peter Crouch, who made a big impact as a substitute on his debut.
Barnes took responsibility and coolly slotted home the equaliser as he became the first Burnley player since the departed Sam Vokes at Everton in April, 2017 to score from the spot in a top-tier fixture.
And it was no more than the Clarets deserved from a storming late fightback as they peppered the Southampton penalty area to ease some of the pain of being on the end of a last-ditch leveler at Manchester United in mid-week.
With new signing Crouch starting on the bench – alongside the fit-again Robbie Brady – the Clarets were again unchanged following their draw at Old Trafford.
Southampton included Danny Ings as the on-loan striker returned to face his former club for the first time, his previous trip back to Turf Moor seeing him sit on the Liverpool bench.
His afternoon was sadly to last no more than 27 minutes as he succumbed to another injury problem, but by then he should have put the Saints ahead.
In a decent start from the visitors, Matt Targett curled a lovely ball in behind the Clarets’ back line but Ings was unable to beat Tom Heaton, who stood tall to make a crucial block.
It took the best part of half an hour for the Clarets to start to pose a sustained threat, but they could then have led in a controversial finish to the opening half.
There had been a chance for Chris Wood, who turned smartly inside Stephens before lifting his effort over the bar and Barnes and Jack Cork had efforts blocked following Burnley’s first corner of the afternoon.
But the major talking point came 12 minutes before the break when the Clarets were again denied a penalty and Barnes was booked for diving.
The striker’s touch from a long ball forward from Phil Bardsley had taken the ball away from goalkeeper Alex McCarthy.
The keeper’s momentum that carried him into Barnes, who was upended.
But rather than point to the spot and end the long wait for a penalty, referee Anthony Taylor penalised Barnes for simulation.
Taylor, having failed to book Southampton midfielder Callum Slattery for catching Charlie Taylor with a late challenge in the aftermath of Ings’ chance, then cautioned Bardsley as a sense of injustice pervaded Turf Moor.
And with the Clarets seemingly knocked out of their stride, it was no surprise when Southampton went ahead 10 minutes into the second half.
James Ward-Prowse had seen one header well saved by Heaton, but the Clarets’ skipper was beaten when Redmond, seemingly revitalised by the arrival of Ralph Hasenhuttl as manager, ran at the Burnley defence before firing into the bottom corner from 25 yards.
Dyche almost immediately sent on winger Johann Berg Gudmundsson to increase the Clarets’ attacking options and from the Icelander’s corner, James Tarkowski connected with a header which McCarthy had to palm away.
The Clarets tried to wind it up as they forced Southampton back and with 15 minutes to go, Crouch was sent for his debut.
And the former England man made an instant impact, causing confusion in the visitors’ penalty area from Bardsley’s ball in to help make an opening for Barnes, who was denied by a fine block from McCarthy.
Burnley were virtually camped in the Saints’ half and with eight minutes to go were only inches away from an equaliser, with Barnes again the central character.
A cross from Taylor was headed down by Gudmundsson and Barnes connected superbly with a volley which crashed against the bar.
Southampton’s only away defeat since Hasenhuttl took over in December came in the Austrian’s first game in charge and they were determined not to let that record go with some disciplined defending.
But the Clarets’ pressure finally paid off deep into four minutes into added time when Crouch punished one of his former clubs, forcing the penalty which Barnes gleefully tucked away to keep Burnley's momentum going.
Burnley: Heaton; Bardsley, Tarkowski, Mee, Taylor; Hendrick (Gudmundsson 59), Westwood, Cork, McNeil (Brady 81); Wood (Crouch 76), Barnes. Substitutes: Hart, Gibson, Ward, Vydra.
Booked: Barnes, Bardsley
Southampton: McCarthy; Bednarek, Stephens, Vestergaard; Romeu; Ward-Prowse, Slattery, Armstrong (Valery 77), Targett; Ings (Long 27), Redmond (Austin 87). Substitutes: Gunn, Elyounoussi, Jones, Sims.
Referee: Anthony Taylor