South Korea international Heung-Min Son gave Spurs an early lead, but two goals from Northern Ireland captain Steven Davis saw the Saints take the three points back to the South Coast.
Son strikes first as Spurs start well
The hosts took the lead on 16 minutes after a mix-up in the Southampton defence, as Son found himself in space but with an advancing Fraser Forster heading towards him.
The English keeper failed to claim the ball and Son rounded him, before fooling Cuco Martina into a sliding challenge to give the himself an empty net and put Pochettino's men 1-0 up.
Saints strike back
After a poor start from Saints, the visitors grew into the game and levelled proceedings just after the half-an-hour mark. Attacking midfielder Davis received a cut-back from Dusan Tadic before turning the ball neatly past Hugo Lloris in the Tottenham net.
Spurs almost regained the lead in first-half stoppage time. Jose Fonte was robbed of the ball by a golden-boot chasing Harry Kane but the English striker couldn't convert due to what would be a game-defining stop by Forster.
As the second half went on, neither side could really carve out any clear-cut opportunities of note, the closest either side came to finding the back of the net being when Spurs defender Jan Vertonghen saw his header cleared off the line.
Davis at the double
On 72 minutes Southampton took the lead for the first time. Davis managed to wriggle past a few Tottenham challenges after a neat one-two at the edge of the area before slotting the ball in the bottom right-hand corner to send the Southampton fans wild.
Southampton saw the game out comfortably and Tottenham didn't really pose any threat to Forster's goal bar an Erik Lamela free kick which was fired over the top, but never troubling the England international.
Plenty to decide in final week
The result sees Southampton continue their quest for European qualification as their excellent 2016 form continues, but their fate remains out of their own hands for the time being.
Spurs, meanwhile, will look to confirm a second-placed finish with a win over Newcastle United on the final day, with the Magpies possibly being relegated before then depending on results elsewhere.