The 22-year-old Algeria international moved to the German side on a season-long loan in August and has made 20 Bundesliga appearances.
He has agreed a four-year deal with the Gelsenkirchen team, although neither club has revealed details of any fee.
Bentaleb had made 66 appearances for Spurs since joining as a teenager.
Tottenham Hotspur midfielder Nabil Bentaleb will join Schalke on a permanent deal at the end of his loan spell this summer.