The SA National Roads Agency Ltd (Sanral) will be repositioned and CEO Nazir Alli will remain at the helm, said Transport Minister Sibusiso Ndebele on Thursday.
Alli tendered his resignation as CEO earlier in the month, but on Thursday it was announced he would stay on.
He quit after a ruling by the High Court in Pretoria halted e-tolling pending a full judicial review.
Ndebele said Sanral's mandate should be broadened and the organisation repositioned so that it could provide support to provinces where capacity remained a problem.
"We cannot have as a country a good national road network whilst provincial and municipal roads remain in a sorry state," he said.
Alli's "institutional memory" would help with this repositioning. The mandate and responsibilities of Alli's position would be reviewed. This process would inform the drafting of a new contract of employment.
An inter-ministerial committee was set up after the court ruling to handle the Sanral matter.
Ndebele said this committee was concerned by the impact Alli's departure would have had, given his involvement in the process.
"The Sanral CEO was subsequently requested to withdraw his resignation in the interest of continuity at Sanral," the department said.
Earlier, Deputy President Kgalema Motlanthe said Alli would "stay put".
"There is no search for a new CEO," Motlanthe told reporters in Cape Town.