The 29-year-old, who spent three months on loan at Elland Road at the end of last year, has signed a two-and-a-half year contract. Manager Neil Warnock, who was in charge of Tonge during their time together at Sheffield United, sees the experienced Mancunian as having a pivotal role to play during the second half of the season as Leeds look to mount a promotion challenge.
"Tongey showed what an important member of the squad he is," Warnock told the club's official website. "I'm delighted we've been able to agree things with Stoke to bring him here permanently."
He added: "I think people saw Michael get better as time went on and you could see what he brought to the side."
Tonge made 22 appearances for Leeds between September and December and scored five goals, including stunning strikes at both Bristol City and Sheffield Wednesday.
He made over 260 appearances for Sheffield United before a reported £2million fee took him to Stoke in the summer of 2008, but he struggled to establish himself as a first-team regular at the Britannia Stadium and had loan spells at Preston (twice), Derby and Barnsley before teaming back up with Warnock at Elland Road.