Cape gooseberry production has been limited by vascular wilt caused by Fusarium oxysporum f. sp. physali (Foph). Fusaric acid (FA) is a mycotoxin produced by many Fusarium species such as F. oxysporum formae speciales. The effects of the interaction between this mycotoxin and plants (such as cape gooseberry) under biotic stress (water deficit, WD) have been little explored. Three experiments were carried out. The objectives of this study were to evaluate (i) different Foph inoculum densities (1 × 104 and 1 × 106 conidia ml−1; experiment (1); (ii) the effect of times of exposure (0, 6, 9, and 12 h) and FA concentrations (0, 12.5, 25, 50, and 100 mg L−1; experiment (2), and (iii) the interaction between Foph (1 × 104 conidia mL−1) or FA (25 mg L−1 × 9 h), and WD conditions (experiment 3) on the physiological (plant growth, leaf stomatal conductance (gs), and photochemical efficiency of PSII (Fv/Fm ratio) and biochemical [malondialdehyde (MDA) and proline] responses of cape gooseberry seedling ecotype Colombia. The first experiment showed that Foph inoculum density of 1 × 106 conidia ml−1 caused the highest incidence of the disease (100%). In the second experiment, gs (~40.6 mmol m−2 s−1) and Fv/Fm ratio (~0.59) decreased, whereas MDA (~9.8 μmol g−1 FW) increased in plants with exposure times of 9 and 12 h and an FA concentration of 100 mg L−1 compared with plants without FA exposure or concentrations (169.8 mmol m−2 s−1, 0.8, and 7.2 μmol g−1 FW for gs, Fv/Fm ratio and MDA, respectively). In the last experiment, the interaction between Foph or FA and WD promoted a higher area under the disease progress curve (AUDPC) (Foph × WD = 44.5 and FA × WD = 37) and lower gs (Foph × WD = 6.2 mmol m−2 s−1 and FA × WD = 9.5 mmol m−2 s−1) compared with plants without any interaction. This research could be considered as a new approach for the rapid scanning of responses to the effects of FA, Foph, and WD stress not only on cape gooseberry plants but also on other species from the Solanaceae family.