The former Kaizer Chiefs midfielder joined the National First Division side last season to work with coach Sello Chokoe.
Reports suggest that Chokoe and Mathebula were given an ultimatum to win the next two games or face the axe.
However, Mathebula dismissed these rumours, saying he wanted to be closer to his family.
“Yes I did resign today from the team, I have family issues that needs my attention as you know my family is in Johannesburg and I was here but my family issues need me to be close hence my resignation. It unfortunately happened fast and I couldn’t tell my team early but there was nothing I could do at the point I need to be there for my family,” Mathebula told Limsportszone.
“I will be forever be grateful to the Chairman, Masala Mulaudzi for the opportunity and the rest of the team. I am also very grateful to coach Sello Chokoe for what he also taught me and the whole technical staff.”