With Arsenal's third place finish ensuring Champions League football for Arsene Wenger's side, their Europa League spot for winning the FA Cup goes to the next highest placed Premier League side, which is seventh-placed Saints.
Ronald Koeman's outfit will enter the competition at the third qualifying round, with the first leg on July 30.
Southampton last entered Europe 12 years ago after they lost to the Gunners in the final of the FA Cup and this is the first season that the European place has gone to the next-best Premier League side rather than the losing finalists.
The Saints will join Liverpool, Tottenham and West Ham in next season's competition.