With the wind swirling and rain lashing down, a stunning early free-kick from England hitman Rickie Lambert gave the home side the early advantage before three goals in six minutes changed the course of the match.
Stoke deservedly levelled thanks to new-signing Peter Odemwingie, who latched onto a wonderful through-ball from Charlie Adam to open his Potters account.
But the visitors weren't level for long after Steven Davis' wind-assisted cross flew straight in to put the Saints back in front.
However, another excellent Adam assist helped Peter Crouch bundle the visitors level just before half-time from a corner.
Neither side could find a winner in a treacherous second half, and the game finished level for the fourth successive meeting of these two sides in the Premier League - a result that will please Mark Hughes more, as Mauricio Pochettino's men have now won just once in their last seven at home.
The windy conditions looked set to disrupt much of the play, but both sides passed and moved with conviction, which made for an entertaining game right from the word go.
Southampton started brightly and went ahead early on. Adam needlessly handled on the edge of the box, allowing Lambert the opportunity from the free-kick, which he took with both hands, curling a sublime effort past Begovic from a tight angle.
The goal did spark the visitors into life, but the aerial route they were adopting was being dealt with by the Saints' rearguard time and again.
However, a goal of real brilliance got the Potters back on level terms. Adam was given time and space in his own half, and picked a pinpoint through ball to play in Odemwingie, who slotted past the onrushing Boruc to restore parity.
And the visitors seemed buoyed by that rare away strike, after failing to score in five of their previous six, looking eager for more, but were stung by a moment of fortune for the home side.
Davis received a throw-in on the right, cut inside, and whipped a great cross in, which evaded everyone and bounced past Begovic, with a great deal of wind assistance, into the net.
However, that lead lasted only three minutes, and Adam again was key. His precise corner was bundled in by Crouch, who scored against one of his many former clubs.
The second-half was a completely different story, as the rain intensified, it became more difficult for both sides to keep control of the ball.
Stoke adopted a much more defensive approach, and were very solid in repelling wave after wave of Southampton attacks.
Begovic remained relatively untroubled in the Potters' goal though, but for a few crosses and high balls to deal with, and never looked like conceding again.
Stoke did still offer some threat on the break, but produced a vastly improved performance on the road, and looked like a different side after that morale-boosting win over champions Manchester United last time out.