Mabaso, 27, and Fita Khupe, 61, are accused of murdering seven members of the Khoza family in October.
The police found the bodies of three women and four children buried under sand in a house in Vlakfontein on October 29 after neighbours noticed a stench coming from the house.
Mabaso was also facing three counts of rape.
The case against the men was due to sit in the Protea Magistrate’s Court on Thursday.
Mabaso died on Friday, police spokesperson Kay Makhubele told News24 on Thursday.
Makhubele said the suspect was booked out of prison by police officers for “further investigations” and died while in holding cells at Cape Town Central Police Station.
Makhubele could not immediately say why Mabaso was taken to Cape Town for “further investigations” and what the details of those investigations were.