As the use of medicinal plants continues to gain popularity worldwide, there is dire need for herbal medicines to be guaranteed in their safety and efficacy. South Africa has a largely under-explored medical flora scientifically due to the vast number of plant species that are consumed for medicinal purposes by the public, creating an urgent need to better define plants with therapeutic effects. To meet these aims, a combination of high-throughput analytical techniques that are sensitive and versatile are used for the standardization and authentication of commercialized natural products as part of quality control regimes. These methods also serve to highlight the role of analytical methods in providing accurate and reliable information pertaining to the biochemicals of medicinal plants in those species whose chemistry remains partially understood or poorly characterized. The review highlights the advancements made in analytical technology for the assessment of biochemical profiles, biomarker compounds and quality control in chosen commercialized products, produced from indigenous South African species. We also summarize studies on the phytochemistry, pharmacology, clinical trials and available patents associated with some of South Africa’s medicinal plants where commercialization has occurred or is imminent. This was achieved through a detailed literature search using web-based database searches including Google Scholar, Scopus and Web of Science (WoS) as well as ethnobotanical literature on South African medicinal plants. Bibliometric analysis was performed on the data mined from WoS. It is clear that future advancements and further development of the natural products industry in South Africa will benefit from a diverse range of technological approaches.