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.