Ramaphosa must now cement control by garnering a majority in the 80-member National Executive Council (NEC), whose election takes place every five years, as it could still cause him trouble if it houses many of his political enemies.
On Monday, he defeated former health minister Zweli Mkhize by around 57% to 43% in a two-horse race to secure a second five-year term as ANC leader.
His re-election, despite a scandal dubbed "Farmgate" by the media over cash hidden on the president's private farm, paves the way for him to run for a second term in 2024. Ramaphosa has denied any wrongdoing.
The cash scandal remains a cloud over Ramaphosa, who has challenged in court an investigation report that said he might have committed misconduct. He has not been charged with any crime, but some opponents had called for his resignation.
It had raised questions about how Ramaphosa, who came to power on a promise to fight graft, had acquired the money and whether he had declared it.
Several investigations, including by the police, the South African Reserve Bank and the Directorate for Priority Crime Investigation, are still on.
Should any of the probes find evidence against Ramaphosa, he could face the risk of being removed from the presidency by the all-powerful NEC.
"Since the NEC has the power to recall an ANC president, Ramaphosa will need to ensure that his allies win a majority of seats in the body to stave off the threat of removal," Eurasia Group said in a note.