Under pressure after last month's unrest claimed 354 lives, Ramaphosa said he was abolishing the security ministry and placing the "political responsibility" of the spy agency under his office.
"This is to ensure that the country's domestic and foreign intelligence services more effectively enable the President to exercise his responsibility to safeguard the security and integrity of the nation," he said in a televised speech.
The move comes in the wake of what he described as an "orchestrated campaign of public violence, destruction and sabotage" that broke out after his predecessor Jacob Zuma was jailed for 15 months for ignoring a judicial investigation into corruption while in office.
Thousands of businesses were looted and destroyed over several days forcing the government to deploy 25,000 soldiers to help restore order.
The National Assembly speaker Thandi Modise is named the new defence minister.
Ramaphosa also replaced the country's health minister Zweli Mkhize, widely respected for his handling of the coronavirus pandemic, but who is shrouded in an alleged corruption scandal involving coronavirus communications funding.
Ramaphosa said Mkhize had asked to "step down…in order to bring certainty and stability to this important portfolio" and was replaced by Joe Phaahla, who until now had been the deputy health minister.
Mkhize, 65, was placed on special leave early in June after graft investigators opened a probe into a 150 million rand ($10,4 million) health ministry communications contract.
Mkhize, who had been health minister since 2018, has denied any involvement with the Digital Vibes contract.
His case was one of over 4,000 coronavirus-linked contracts being investigated for alleged graft by the government's Special Investigation Unit.
Last week the unit approached the country's prosecuting authority in an effort to recover funds paid to the communications firm Digital Vibes, owned by Mkhize's close associates.
A local national newspaper the Daily Maverick reported that some of the communication funds were syphoned toward a new upmarket nail bar run by Mkhize's daughter-in-law, which was opened in December.
Some of the funds reportedly funded a hair salon said to be owned by his son Dedani, who has denied benefiting from the anti-virus funds.
Mkhize gained popularity and respect through his strategic and skillful handling of the pandemic in Africa's worst hit country.
The doctor-turned-politician and former treasurer of the ruling ANC had before the scandal been touted as one of the potential successors to Ramaphosa.
Finance Minister Tito Mboweni, who he said had long asked to step down, was replaced by Enoch Godongwana, ANC's head of economic transformation subcommittee and chairman of the Development Bank of Southern Africa.
Ramaphosa took the reigns of power in 2018 following Zuma's forced resignation by the ruling African National Congress (ANC), pledging to root out the corruption that is blamed for undermining the economy of Africa's most industrialised country.