Barton came off the bench with 20 minutes to play and it only took him a matter of minutes to make an impact, as his low free kick beat Fraser Forster.
The defeat means Southampton have not won in the league since the December 18th.
More fouls than shots
The first half failed to provide many notable efforts and the main talking point was probably the amount of questionable fouls from Burnley's players.
Shane Long was kneed in back by George Boyd. After Jeff Hendrick appears to lead with his elbow and Barnes was penalised for catching Romeu with an arm.
Southampton's best chance fell to Dusan Tadic, who was played through by Nathan Redmond, but only dragged the shot wide when he should have done better.
A ball crossed in by Long was met by James Ward-Prowse, who headed down towards goal forcing Tom Heaton into a save, Tadic's rebound was cleared off the line by Ben Mee.
Neither side take control
Hendrick produced the first effort of the second half, as he hit a long range effort wide of the target.
Barnes found himself running through towards goal, as Oriel Romeu attempted to win the ball behind and bundled him over, but once again Burnley failed to do anything with the set piece.
Pierre-Emile Hojbjerg then had a go with a raking shot, which was deflected twice before going out for a corner.
The game continued to offer few chances at both ends but Steven Defour nearly broke the deadlock with a long range effort, before Burnley had to scramble the ball away from their goal after Virgil van Dijk squared the ball across the six yards box.
Welcome home, Joey
Barton was introduced in the 72nd minute and it didn't take him long to make a mark on the game.
The midfielder stood over a free kick around 25 yards out from goal and as the wall jumped, Barton curled a low effort past Forster, who should have done better.
It goes without saying that the roof was well and truly blown off Turf Moor and Barton looked delighted as his teammates surrounded him.
Heaton keeps them out
Southampton tried to level the tie but Heaton kept out van Dijk's header before making a double save from Jay Rodriguez and Josh Sims.
The results puts Burnley above Southampton in the table and means they have now won eight matches at home this season.
The Saints sit 12th in the table.