The resignation of Ramathlodi on Wednesday comes almost a week after his former Cabinet colleagues Tina Joemat-Pettersson, Dipuo Peters and Mcebisi Jonas quit.
However, former Finance Minister Pravin Gordhan and ex-Tourism Minister Derek Hanekom have stayed on as ANC MPs.
Ramathlodi was the Premier of Limpopo between 1994 and 2004.
He then came to Parliament in 2009 where he first served as chairman of the portfolio committee on justice.
He was then appointed as Mineral Resources Minister in May 2014.
Zuma then later moved him to Public Service and Administration after the death of Collins Chabane in 2015.