Former club "coach" Jerry Richardson testified that Madikizela-Mandela decided to kill Seipei to cover up what had happened.
The Mandela crisis committee, made up of church, community and ANC leaders, was formed to secure the release of four boys, including Seipei, who were abducted from Methodist minister Paul Verryn's manse in late December 1988.
"I slaughterd him (Seipei) like a goat," Richardson said, as Seipei's mother, Joyce, left the hearing hall in tears.
Richardson said he abducted Seipei on Madikizela-Mandela's instructions after Verryn was falsely accused of sodomising the boys.
Richardson was led through his testimony by his lawyer, Tony Richards (correct).
Richardson said: "I killed Stompie under instructions of Mami (Madikizela-Mandela)."
He said he and another football club member, "Slash", went to look for a place where they could kill Seipei. They decided on a rocky patch of ground near a railway line in Noordgesig, Soweto.
Richardson said the plan to kill Seipei, several days after the abduction and assault, had to be postponed because a lot of visitors, including the crisis committee, kept coming to Madikizela-Mandela's house.
Richardson said the visitors included former South African Council of Churches' secretary-general Frank Chikane.
Richardson said Madikizela-Mandela hid him (Richardson) so the visitors could not speak to him.
"Mami was concerned the crisis committee would discover the presence of the youth in her yard," Richardson added.
He said Seipei was more severely beaten than the other three youths because Madikizela-Mandela accused him of being an impimpi (police informer).
"Stompie was tortured so severely... I could see he would ultimately die," Richardson said.
He said Madikizela-Mandela had participated in the beating, punching the youths with her fist. The youths were later sjambokked and lifted into the air and dropped onto the concrete floor.
Richardson said the football club had tortured youths in "horrible, brutal ways... in the manner used to torture freedom-fighters (by the police)".
A few days later, Richardson and "Slash" took Seipei to the site in Noordgesig they had chosen. Richardson said he had to help Seipei walk because "he was very sick and very weak".
When they reached the site, Richardson said he made Seipei lie on his back and separated a pair of garden shears.
He said he stabbed Seipei in the neck. "I put the shears through Stompie's neck. They went to the back... It was a stabbing motion, not a cutting motion," Richardson said when asked precisely how he had killed Seipei. He pointed to behind his right ear as he spoke.
On Tuesday, senior state pathologist Dr Patricia Klepp said that during her autopsy of Seipei's body, she found two stab marks behind Seipei's right ear and a larger stab mark on the left side of his neck.
On Wednesday Richardson said "Slash" made cutting motions with his half of the garden shears, because he wanted to make sure Seipei was dead.
He said they waited for a long time to make sure Seipei was dead. "We told ourselves we were committing the perfect crime."
They then washed their clothes in a nearby river and returned to Madikizela-Mandela's house, placing the garden shears back in the garage.