Federico Fernandez fired Newcastle into the top half of the table with a comeback win inspired by two Steve Bruce substitutions.
The Toon looked like they were falling to their first home Premier League defeat since the opening day when Danny Ings scored for the fifth game in a row.
But Jonjo Shelvey levelled for the hosts from a cross by sub Andy Carroll.
Then three minutes from time, Saints stopper Alex McCarthy spilled replacement Sean Longstaff’s shot, allowing Fernandez to pounce for the winner.
Newcastle’s second straight win moves them up to tenth.
While the late heartbreak for Southampton means they missed the chance to move out of the bottom three.
In a dull first half, Allan Saint-Maximin, who got Newcastle’s opener at Sheffield United on Thursday, was once again boss Bruce’s most lively player.
On one mazy run, the Frenchman beat three players but his pull back was cut out by James Ward-Prowse before Miguel Almiron could pull the trigger.
But the Toon offered very little else going forward.
And, just like in Sheffield in midweek, they were once more indebted to Martin Dubravka for keeping the scores level going into the break.
Nathan Redmond was through on goal after cutting out Jetro Willems’ sloppy pass and skipping past Fernandez, but Dubravka saved with his feet.
Then from the resulting corner, Newcastle’s keeper beat away Redmond’s powerful drive.
But even Dubravka could not rescue the Toon following a defensive mix-up seven minutes after the break.
Jack Stephens launched a long ball over the top and with half-time sub Fabian Schar inexplicably ducking under it, Ings got the other side of Fernandez and slotted past Dubravka.
Ings’ strike made him the first Saints player to score five in a row in the Premier League since James Beattie in 2003.
And the visitors almost doubled their lead when Cedric Soares had a strike saved by Dubravka, before Moussa Djenepo headed the resulting corner wide.
But out of nowhere, Newcastle levelled after 69 minutes.
Carroll, who had replaced the woeful Joelinton, hooked a cross in from the right.
And in a crowded box, Jonjo Shelvey jumped the highest to head past Alex McCarthy and score for the third match running.
There was to be one final twist – and it was another of Bruce’s subs who made an impact.
Longstaff had only been on the pitch two minutes when he tried his luck from 25 yards.
And McCarthy made a mess of his shot, parrying the ball straight to Fernandez, who slotted the winner into an empty net.