Police have charged the couple, who were running the facility from a church, with kidnapping. Additional charges may follow. The pair have not yet commented publicly.
During the raid, officials found a 16-year-old girl and an 11-year-old boy being kept in the same room as adults. The Department of Social Development said the conditions were appalling.
Illegal rehabilitation centres have proliferated in South Africa in recent years as drug use has increased across the country. Last year, the department reported it had uncovered more than 100 unlawful facilities operating nationwide, mostly in Gauteng province, which includes Johannesburg.
The discovery in Mpumalanga highlights the ongoing problem of unregulated centres that pose as treatment facilities but instead subject vulnerable people to abuse and captivity. Authorities have not released details about how the individuals were recruited or how long they had been held.