The National Prosecuting Authority's Missing Person Team exhumed the bodies Tuesday, The Star newspaper of Gauteng, South Africa said.
The remains are believed to belong to Lono Sono and Siboniso Shabalala, who disappeared in 1988.
Sono's father, Nicodemus, testified in 1996 that Madikizela-Mandela told him she was taking her son away because he was a spy, The Star said. The next day, Shabalala was abducted and, two days later, the bodies of two unidentified men were found.
Authorities said they are hoping to identify the remains and further investigate the case but wouldn't comment on whether Madikizela-Mandela is a suspect.