Derby and her senior management team have been under pressure from miners, industry bodies and labour unions over the deteriorating performance of the freight rail utility.
Miners say Transnet's underperformance has cost mineral exporters billions of rand in potential revenue.
Transnet, whose flagship freight rail service has struggled due to the shortage of locomotives and spares and cable theft and vandalism of its infrastructure, slumped to a R5.7bn ($302m) loss in the year ended 31 March.
South African telecoms company Telkom said in a separate statement that it had appointed Dlamini as its CFO.
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