The England international was a free agent following his release from Manchester United at the end of last season and has agreed a one-year pay-as-you-play deal at the Britannia Stadium.
Owen, 32, was unveiled as Stoke manager Tony Pulis' seventh summer signing but both the player and the club were made to sweat on a decision from the Premier League to confirm his eligibility.
The deal was announced by the club on Tuesday but remained subject to confirmation that the Potters submitted the relevant paperwork prior to the 4pm deadline for the player to be signed on a free agent basis.
The uncertainty meant the Premier League were only able to release the official 25-man squads for 19 of the 20 clubs.
But now a decision has been made and Owen will be available for selection ahead of Stoke's next Barclays Premier League fixture, which sees champions Manchester City visit the Britannia Stadium.
Forward Owen, who has also played for Real Madrid and Newcastle, was linked with a return to former side Liverpool as a solution to their goalscoring worries.
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But it is Pulis who has signed Owen on a performance-related contract following the arrivals of Jamie Ness, Geoff Cameron, Michael Kightly, Maurice Edu, Charlie Adam and Steven N'Zonzi at the club over the course of a busy summer.
A Premier League statement read: "The Premier League board has confirmed to Stoke City the registration of Michael Owen. Consequently he can be included in their 25-man playing squad."
Owen confirmed the news himself on Twitter moments before the club posted the decision on their official website.
His Tweet read: "It's official! Deal done. I'm a Stoke player. Can't wait to get going."