This was confirmed by Wits coach Gavin Hunt on Monday after he was named the coach of the month for February.
Hlatshwayo was recently linked with a big move to Soweto giants Orlando Pirates, but has put that to bed by extending his contract with the Absa Premiership defending champions.
“He has signed the extension now, so that was put to bed,” Hunt said.
“He has signed another three years, so yeah. I know and I read about it [rumours of joining Pirates] and obviously it didn't make the boy's life easier because he was getting phone calls or whatever.
“He is okay and he is settled now.”
Hlatshwayo's contract with the Clever Boys was set to expire next year in June.
Hunt also confirmed that another defender Buhle Mkhwanazi has extended his stay with the team and that they are also talking to other players whose contract is up at the end of the season.
“Buhle as well he is fine. He got an extension, those are fine.
“You always got to try and work six to eight months in advance. I think if you don’t and you wake up you get lost.
“We always try to work in advance even though you are worried about the situation but you need to work in advance, that's the nature of the game.”