The drone hovered over St Mary's Stadium as the players made their way to the dressing room at the behest of police and security staff.
They remained around seven minutes before the arena was deemed secured and play could resume.
Aston Villa could then hit their free kick at 0-0.
Jokes rained down on Twitter
The jokes started pouring in on Twitter.
"The drone was sent in to save Southampton," was one of those where most mocked the tactically defensive move that favored Southampton.
The Villa fans chanted in the direction of the drone: "You've only come to see Villa!"
A similar incident occurred a year ago when the Premier League match between Brentford and Wolverhampton was paused for 20 minutes after a drone came in over the pitch.