Everton midfielder Ross Barkley has signed a new four-year deal with the club.
The South Africa international will return to the Championship following previous loan spells in the division with Preston and Reading.
Khumalo, 26, joined Spurs in the 2011 January transfer window but is yet to make a senior appearance for the club.
He spent last season on loan at Greek club PAOK Salonika.
"I'm very pleased to be here," Khumalo told the Doncaster website. "I'm very happy that things have worked out and I'm just looking forward to the start of the season.
"All the lads have been really welcoming, which really helps. I've had a lot of support from the skipper and everyone has made it really easy to make the transition."