His horrified mum called cops after witnessing the gruesome slaughter.
But officers said he was tucking in to Thembisa's raw flesh by the time they turned up. He then attacked them with a knife before being shot, said police Captain Edith Mjoko.
Mapekula reportedly killed a woman and then attempted to eat her before police shot him.
Mapekula's devastated mother said: "I never raised a son like this one. I never imagined this."
Police originally said Mapekula had dragged Thembisa from the street before butchering her.
But neighbours said she did odd jobs at his home and was washing in the back yard when he attacked her.
Captain Mjoko said: "He killed her with a knife by cutting her throat.
"When the mother of the suspect saw what was happening she rushed and called the police to the scene.
"When they arrived the suspect was busy eating the flesh of the deceased.
"Police ordered him to stop and to hand himself over.
"He went berserk and stormed at them with the knife.
"Several warning shots were fired to deter him but in vain."
Mayor Bulelwa Mabengu suspected Mapekula could have been under the influence of drugs.
"I believe that drugs and substance abuse was a major contributing factor and yearn to call upon law authorities to show a more proactive visibility in our area," she told RNews.
Mapekula was under police guard when he died at Nelson Mandela Hospital, Mthatha.
Hospital spokesman Sizwe Kupelo told TimesLive: He was transferred with gunshot wounds and needed emergency surgery. But he unfortunately died."
It is the second cannibal horror case to hit South Africa in three weeks.
Six men are in custody after a woman was reportedly raped, murdered and butchered before parts of her were eaten in Estcourt.
Police investigating the tribe of cannibal witch-doctors have found eight human ears in a cooking pot as it emerged villagers were coerced into eating flesh because it would make them bulletproof.
The suspects were arrested after one of the men walked into a police station with a piece of an arm and a leg saying he had lost the taste for human flesh.
It prompted villagers in Estcourt, South Africa, to hold a meeting, where 300 residents allegedly admitted eating humans and digging up graves.
Grim details of the case have emerged as the spiritual healers' homes were raided with officers discovering a number of severed body parts and human remains stuffed inside suitcases.
