The midfielder has joined the club on a two-and-a-half-year-deal for an undisclosed fee.
Tonge spent time on loan with the Whites from September and made 22 appearances for the club.
The 29-year-old scored five goals during his loan spell with most remembering his dramatic equaliser against Sheffield Wednesday.
Neil Warnock has already managed to bring in Ryan Hall on a permanent deal, and he told the club's official site he was delighted to complete the deal.
"Tongey showed what an important member of the squad he is. I'm delighted we've been able to agree things with Stoke to bring him here permanently.
"I think people saw Michael get better as went on and you could see what he brought to the side."