Background Estimates of the disease burden associated with different respiratory viruses are severely limited in low- and middle-income countries, especially in Africa. Methods We estimated age-specific numbers and rates of medically and non-medically attended influenza-like illness (ILI) and severe respiratory illness (SRI) that were associated with influenza, respiratory syncytial virus (RSV), rhinovirus, human metapneumovirus, adenovirus, enterovirus and parainfluenza virus types 1-3 after adjusting for the attributable fraction (AF) of virus detection to illness in South Africa during 2013-2015. Rates were reported per 100,000 population. Results The mean annual rates were 51,383 and 4,196 for ILI and SRI, respectively. Of these, 26% (for ILI) and 46% (for SRI) were medically attended. Among outpatients with ILI, rhinovirus had the highest AF-adjusted rate (7,221), followed by influenza (6,443) and adenovirus (1,364); whereas, among inpatients with SRI, rhinovirus had the highest AF-adjusted rate (400), followed by RSV (247) and influenza (130). Rhinovirus (9,424) and RSV (2,026) had the highest AF-adjusted rates among children aged <5 years with ILI or SRI, respectively; whereas rhinovirus (757) and influenza (306) had the highest AF-adjusted rates among individuals aged ≥65 years with ILI or SRI, respectively Conclusions There was a substantial burden of ILI and SRI in South Africa during 2013-2015. Rhinovirus and influenza had a prominent disease burden among patients with ILI. Rhinovirus had the highest burden of illness among patients of any age with SRI, followed by RSV. RSV and influenza were the most prominent causes of SRI in children and the elderly, respectively.