Jatropha podagrica holds a longstanding place in traditional herbal medicine, primarily utilized for addressing skin infections, acting as antipyretics, diuretics, and purgatives. In this study, our primary objective was to investigate the secondary metabolites present in J. podagrica leaves, with the aim of pinpointing natural compounds exhibiting potential antiviral activities. Five secondary metabolites (1–5), including an auronol glycoside (1), two coumarins (2 and 3), a chromane (4) and a gallotannin (5), were isolated from J. podagrica leaves. Compound 1 presented as an amalgamation of unseparated mixtures, yet its intricate composition was adroitly unraveled through the strategic deployment of a chiral HPLC column. This tactic yielded the isolation of epimers (+)-1 and (−)-1, ascertained as unreported auronol glycosides. The structures of these novel compounds, (+)-1 and (−)-1, were elucidated to be (2S)-hovetrichoside C [(+)-1] and (2R)-hovetrichoside C [(−)-1] through NMR data and HR-ESIMS analyses, enzymatic hydrolysis, and comparison of optical rotation values. Cytotoxicity and antiviral effects were assessed for the isolated compounds ((+)-1, (−)-1 and 2–5), along with compound 1a (the aglycone of 1), in the A549 human alveolar basal epithelial cell line. Each compound demonstrated a cell viability of approximately 80% or higher, confirming their non-toxic nature. In the group of compounds, compounds 3–5 demonstrated antiviral effects based on RT-qPCR results, with individual enhancements ranging from approximately 28 to 38%. Remarkably, compound 4 exhibited the most substantial antiviral effect. Utilization of compound 4 to assess immune boosting and anti-inflammatory effects revealed increased levels of STING, RIG-I, NLRP3, and IL-10 along with a decrease in TNF-α and IL-6. Therefore, these findings underscore the potential of these active compounds 3–5 not only as therapeutic agents for SARS-CoV-2 but also as new contenders for upcoming pandemics.