Endophytic fungi have the ability to live inside the host plant tissues without causing neither symptoms of diseases/or harm. Opportunistic infections are accountable for majority of the outbreaks, thereby putting a burden on the health system. To investigate and characterize the bioactive compounds for the control of bacteria of clinical importance, extracts from endophytic fungi were isolated from indigenous South African medicinal plants. Extracts from endophytic fungi were isolated from 133 fungal strains and screened against Gram positive and negative bacteria namely Bacillus cereus, Escherichia coli, Enterococcus faecium, and E. gallinarum using disk diffusion. Furthermore, gas chromatography–mass spectrometry was performed to identify the bioactive compounds. Sixteen out of one hundred and thirty-three (12%) fungi extracts exhibited antibacterial properties against some of the selected bacteria. E. coli was found to be the most susceptible in contrast to E. faecium and E. gallinarum which were the most resistant. The isolate MHE 68, identified as Alternaria sp. displayed the greater spectrum of antibacterial activities by controlling selected clinical bacteria strains including resistant E. faecium and E. gallinarum. The chemical analysis of the extract from MHE 68 indicated that linoleic acid (9,12-octadecadienoic acid (Z,Z)) and cyclodecasiloxane could be accountable for the antibacterial activity. This is the first study conducted on the secondary metabolites produced by endophytic fungal strains isolated from the Pelargonium sidoides DC. possessing antibacterial properties.