It is a surprise reversal of a decision taken on Wednesday to disband rugby's top management team.
Earlier, Van Rooyen's deputy Andre Markgraaff accused him of mismanagement – but the two men would appear to have called a truce.
"We have decided to deal with these issues internally," the SAPA news agency quoted Van Rooyen as saying, who added that the SARU management committee would continue to run "the day-to-day affairs of the union."
Van Rooyen was the only top official not to tender his resignation on Wednesday, following a call by the country's sport minister Makhenkhesi Stofile and the sport's umbrella body for the men to step down.
The call came in the wake of allegations and counter-allegations between Van Rooyen and Markgraaff that came to a head over the weekend when Markgraaff released a "dossier of irregularities" against Van Rooyen.
Markgraaff accused his boss of clinching contracts for a new series between northern hemisphere teams and South Africa without informing his own management team.
There has also been controversy and disagreement over the awarding of the additional franchise for the expanded Super 14 competition, which also involves sides from Australia and New Zealand.
Van Rooyen hit back at Markgraaff by gleaning the support of at least nine of South Africa's 14 rugby provinces.
Observers said months of infighting and power struggles had dented South African rugby's bid to host the 2011 Rugby World Cup.
The International Rugby Board (IRB) council is expected to decide the venue for the 2011 tournament at its November board meeting.
