Mowbray will join the club on 1 July as he serves out his notice at Scottish Premiership club Aberdeen, who finished third this season.
He had been Head of Recruitment with Aberdeen since 2021, and had executive roles at Burnley, Middlesbrough and Leeds United before that.
Mowbray succeeds former Head of Senior Recruitment Joe Shields, who joined Saints from Manchester City last summer before being hired by Chelsea as Co-Director of Recruitment and Talent in October.
The appointment of Mark Bitcon as Director of Performance has also been confirmed.
He joins after two years as Head of Athletic Performance and Innovation at England Rugby. Previously, Bitcon spent four years as Director of Performance Services at Manchester City's Academy.
They are the latest of changes at the top for Southampton, who have just been relegated from the Premier League.
Jason Wilcox joins as Director of Football this summer, with the Manchester City Academy Director's move announced in January.
Following their relegation, the club said in a statement: "We must now reflect on the lessons to be learned from this season and start preparing for the challenges ahead of us in the Championship. Our goal is to return to the Premier League as soon as possible and ensure that we stay there.
"At the same time, we will continue to focus on the long-term development of the club, both on and off the pitch, to ensure its sustainability at the highest level.
"We understand that significant improvement is required, and at the end of the season we will announce our immediate next steps and provide details of how the club will operate moving forward."
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