This after Public Enterprises Minister Lynne Brown announced late on Monday night that Ngubane had tendered his resignation effective immediately. Brown appointed Zethembe Khoza as the interim board chairman until Cabinet approves new appointments.
Numsa second deputy president, Ruth Ntlokotse, said in a statement that the nightmare at the power utility was far from over.
"Whilst we note and acknowledge Ben Ngubane's departure from the Eskom board, he must be held to account for his role as chairperson of Eskom," Ntlokose said.
"His resignation should not exonerate from taking responsibility. We call for an independent investigation into tenders awarded during his tenure, and that where necessary, heads must roll."
Ngubane has indicated that he resigned from Eskom to pursue private business after spending decades in the public sector. Ngubane's resignation took place against a decision by parliament to investigate the power utility, for allegations of mismanagement in issuing government tenders.
Eskom also faced a backlash after reinstating embattled former chief executive, Brian Molefe, who had resigned six months ago and taken a position in Parliament after being named in the Public Protector's "State of Capture" report.
Molefe originally left after the Public Protector raised questions over coal deals between Eskom and a company controlled by the controversial Gupta family, who are wealthy businessmen and friends of President Zuma and employ his son, Duduzane.
"We remain concerned about the bizarre decision which the board took to re-instate former Eskom CEO Brian Molefe, as well as the embarrassing spectacle where the public enterprises minister Lynne Brown at first tried to justify the indefensible by re-hiring Molefe, only for her to be forced to backtrack on the decision shortly thereafter," Ntlokose said.
"The Molefe saga demonstrated very clearly that the board and the ministry are in a state of chaos. The decision demonstrated poor judgement from board members and the minister. Numsa reiterates its demand for the rest of the Eskom board to be removed and for Lynne Brown to be held to account."
Ntlokose said the board of Eskom must be completely transformed and be made up of representatives from civil society, trade unions and business to ensure good governance and transparency.