The 31-year-old has penned a one-year deal with the club with an option to renew.
Nonyane, who has five Bafana Bafana caps, was previously a free agent after his contract with Golden Arrows was not renewed at the end of last season as injuries curtailed his output.
The ex-Jomo Cosmos and Mpumalanga Black Aces defender linked up with Wits on their recent pre-season camp in Durban, and will compete for game-time at Sturrock Park with Wits' Player of the Season Sifiso Hlanti.
"I've signed with Wits and it's one-year and the option to renew," Nonyane tells KickOff.com.
Besides Nonyane, the Students have recruited Vuyo Mere, Simon Murray, Deon Hotto, Haashim Domingo, Gift Motupa, Robyn Johannes, Mxolisi Machuphu, Bantu Mzwakali and Brighton Mhlongo ahead of their season-opener with visiting Free State Stars on Saturday (18h00).
Malawian midfielder Gerald Phiri has also returned from a loan spell at Platinum Stars (now called Cape Umoya United).