Alli would continue in his post until June 3, chairman Tembakazi Mnyaka said in a statement.
The board accepted the resignation at a meeting on Monday.
He thanked Alli for his contribution since Sanral’s inception in 1998. Sanral did not give reasons for Alli’s resignation.
“The immediate focus and priority of the board is to ensure that Sanral continues to perform its essential role in operating and maintaining more than 16,000km of national roads across South Africa,” Mnyaka said.
Processes had been initiated by national government to address the Gauteng Freeway Improvement Project and e-tolling, the start of which was halted by a court order on April 28.
“The board will ensure that Sanral contributes to and co-operates with the deliberations now underway,” he said.