"Eskom board chairman Zola Tsotis has this morning agreed to part ways amicably," said the power parastatal in its Media Desk Twitter feed.
Earlier, Tsotsi said he faced a vote of no confidence by the utility's board late on Monday, after being accused of acting improperly by suspending the chief executive.
Dr Ben Ngubane has been appointed as the utility's acting chairman after Tsotsi agreed to step down to allow the board to focus on the core issues facing the power parastatal, said the utility.
"Dr Ngubane thanked Tsotsi for the selfless decision he took in placing the interests of the company first," said the Twitter feed.
Earlier this month, the utility announced that it was to commission an independent inquiry into the running of the business.
At a media briefing, Tsotsi said that four executives at Eskom had been asked to step aside for the duration of the inquiry. CEO Tshediso Matona was among those asked to step aside.
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