The former England striker has struggled to make an impact for Tony Pulis's side in the Premier League this campaign, scoring one goal during just seven first-team appearances.
The 32-year-old had previously played for Liverpool, Real Madrid and Newcastle before joining the Potters on a one-year deal after leaving Manchester United last summer.
"It is with an immense amount of pride that I am announcing my intention to retire from professional football at the end of this season," he wrote in a statement on his official website.
"I have been very fortunate in that my career has taken me on a journey I could only have dreamed of."
An 18-year-old Owen burst on to the world stage with a memorable goal against Argentina for England at World Cup 1998 in France and has since gone on to win the Premier League, the FA Cup, three League Cups and the UEFA Cup.
The Stoke striker is also the most recent Englishman to win the European Footballer of the Year award in 2001, when he became the first Three Lions player since Kevin Keegan to receive the prestigious accolade.
Owen is England's fourth-highest goalscorer of all time and has totaled 220 goals in his club career to date.