Spokesperson for the police crime prevention unit Superintendent Leon Engelbrecht said the medicines were confiscated in 2000 when two pharmacists and a truck driver were arrested for contraving the Medicines Control Act.
Engelbrecht said Derek Adlam, Deon de Beer and Gilbert Mkize imported counterfeit and substandard medicines from India, among other places, illegally processed the medicines and then distributed it under new brand names countrywide. They were found guilty in March this year and heavily fined. Each was sentenced to five years in prison, suspended for five years.
The medicines included Myprodol, an anti-inflammatory, and Lanzor and Losex, reflux medicines for the treatment of ulcers.
Thousands of boxes of pills were stored in large containers at the Police College in Pretoria.
On Friday the counterfeit products were taken to the CSIR grounds in the Wallmansthal district north of Pretoria, where they were placed in four 3m-deep holes and destroyed in a fire with a temperature of 3 000 degrees Celsius.
Engelbrecht said the incineration took place outside the city to minimize the risk of pollution.
Members of the police commercial crimes unit and organised crime unit took part in the investigation. The huge drug haul and arrests were regarded as some of the most significant in the country's crime history.