The companies named investment chief Ervin Tu, a previous VisionBank manager and Goldman Sachs technology banker, as interim CEO.
The news sent Naspers' shares up 2% on the JSE after trading began on Monday.
The companies did not provide a reason for Van Dijk's departure. However, it coincides with the unwinding Monday of a cross-structure between Prosus and Naspers.
A source close to the company said it was not a major surprise after van Dijk spent a decade at the role, almost double the time most CEOs spend at FTSE 100 companies.
Van Dijk oversaw Prosus's 2019 IPO and the company's stock boomed during the COVID-19 pandemic. However, he struggled to close a valuation gap between Prosus, Naspers and the value of their biggest asset: Chinese software giant Tencent.
Prosus holds a 26% stake in Tencent, which is currently worth around $387bn.
The company now faces a fight to ease the discount between the value of the Tencent stake and Naspers.
In the post-pandemic bust, shares have declined along with a fall in valuation of high-growth technology investments.
More recently, Prosus was forced to dispose of some of its most attractive smaller assets in Russia at a discount in the wake of the invasion of Ukraine.
Van Dijk, who has led Naspers since 2014 and Prosus since 2019, has agreed to remain as a consultant until Sept. 30, 2024, the companies said in a statement.
"The group's strategic goals remain unchanged and it is on target to deliver on its commitments," the global consumer internet companies said in a statement.
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