A notable rise in health-related disability for which evidence-based rehabilitation is beneficial is evident in low-to-middle income countries. This scoping review aimed to systematically identify and map the most common functioning problems associated with health conditions that contribute most to disability in South Africa using the International Classification of Functioning, Disability and Health (ICF) framework. Peer-reviewed evidence published from January 2006 to December 2021 was systematically searched from five databases. Some 268 studies reporting on functioning problems (impairments, activity limitations, and participation restrictions) in South African adults (>18 years) related to 10 health conditions were included. A total of 130 different functioning problems were mapped to the ICF. The most prevalent problems (top 20) were related to mobility, pain, and mental health but spanned across several ICF domains and were mostly in patients at primary care. The high prevalence and wide range of functioning problems may be particularly burdensome on an already strained primary health care (PHC) system. This points towards targeted planning of innovative strategies towards strengthening rehabilitation service delivery at primary care to address these complexities where there is an inadequate rehabilitation workforce.