He was implicated in awarding contracts to a company linked to his stepdaughter, as was facing a new disciplinary inquiry on Friday.
Koko had returned to the power utility after being acquitted in a disciplinary hearing that was largely seen as a "sham".
Eskom spokesperson Khulu Phasiwe confirmed Koko's resignation.
The DA welcomed Koko's "long overdue" resignation but said this does not absolve him from facing criminal charges and allegations brought against him by the party.
The Sunday Times reported in 2017 that Impulse International, a company in which his stepdaughter, Koketso Choma, owned a stake, was awarded tenders worth close to R1bn, allegedly without proper processes being followed. Koko said at the time that he had no influence over the awarding of the tenders.
An internal disciplinary hearing initially found him not guilty on charges he had acted to benefit his stepdaughter. He was later presented with the ultimatum to resign or be fired by the new board - which he flatly rejected.
Source: The Times
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