The 45-year-old Welshman joins from Luton Town after a compensation package was agreed between the Potters and the League One club.
Jones takes over from Rowett, who lasted just eight months at the bet365 Stadium following a poor run of form that has seen Stoke drop into the bottom half of the Championship table.
After enjoying considerable success at Luton – having overseen the side’s promotion to League One last season – Jones is now tasked with returning Stoke to the Premier League.
Stoke owners John Coates and Peter Coates released a joint statement which read: “Nathan is an incredibly driven and passionate individual and we are delighted to have secured his services for Stoke City.
“We have been following Nathan’s career for sometime and when we met him were hugely impressed with his clear vision as to how he will achieve success at Stoke.”
Before taking over at Luton in 2016, Jones worked as an assistant head coach at Brighton, serving under Oscar Garcia, Sami Hyypia and Chris Hughton.
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