King Buyelekhaya Dalindyebo reported to the Mthatha Correctional Centre in Eastern Cape province overnight after failing in an 11th-hour bid to evade incarceration by seeking a retrial or a presidential pardon.
In 2009, the controversial king was convicted of manslaughter, arson and assault charges for offences committed more than two decades ago.
He was sentenced to 15 years in 2009, but in October the Supreme Court dropped the manslaughter charge and reduced his sentence to 12 years on appeal.
"We confirm that King Buyelekhaya Dalindyebo handed himself to the head of Mthatha Correctional Centre," the justice ministry said in a statement.
He is expected to serve his sentence in Wellington Prison, outside Mthatha.
The 51-year-old king, a self-confessed marijuana smoker, was found guilty of torching dwellings that housed some of his subjects and tenants who had resisted eviction.
He was also convicted of publicly assaulting three young men who had already been brutally beaten by his henchmen, and of kidnapping a wife and children of one of his subjects whom he considered a dissident.
It also accused him of "obstructive" action for changing his lawyers 11 times, causing 34 postponements of the case.
Dalindyebo became king of the Thembu, a Xhosa ethnic group that boasted Mandela as its most prominent clan member, in 1989.
The royal family will meet next week to discuss whether a successor should be chosen due to their monarch's imprisonment.
Kings have no official power in modern South Africa, but still command loyalty among millions of people.
Two years ago the king publicly disparaged President Jacob Zuma, an ethnic Zulu, but later apologised.