Bayern Munich sporting director Max Eberl announced the deal on the club's official website: "Daniel established himself immediately as number one in Southampton after his transfer in winter and has found a new sporting home there.
"We thank him for his time in Munich — he is a fantastic character and has always applied himself in a very professional manner. We wish him all the luck in the future."
Peretz, 25, joined Bayern from Maccabi Tel Aviv in the summer of 2023 but was unable to break into a first-team squad where Manuel Neuer and Sven Ulreich sat ahead of him in the pecking order. A loan to Hamburg SV last season produced no Bundesliga appearances before he cut short that spell in January and moved to Southampton.
At St Mary's he was given the opportunity he had been denied in Germany. He made 26 competitive appearances and kept nine clean sheets, forging a strong relationship with head coach Tonda Eckert that proved decisive in his decision to pursue a permanent move.
Southampton, who were relegated from the Premier League last year, begin next season in the Championship.