The consortium based on Trichoderma virens Gl006 and Bacillus velezensis Bs006 was selected in a previous study because the high effectiveness against Fusarium wilt of cape gooseberry (Fusarium oxysporum f. sp. physali—Foph). The compatibility among the strains was determined previously, but the modes of action exerted by the consortium remained unknown. In this study, the modes of action displayed by the Gl006 and Bs006 consortium against the Foph strain Map5 were determined and compared with the modes of action of the single microorganisms. Production of cell wall degrading enzymes (CWDE), cyclic lipopeptides (CLPs) by Bs006 and gliotoxin by Gl006, and fusaric acid (FA) production by Foph were evaluated in the co-culture of the strains in several culture media. Furthermore, the survival of the strains in the soil, the colonization of plant tissues and the induction of systemic responses through a split root model bioassay were evaluated. While Bs006 showed protease, β-1,3-glucanase, and chitobiosidase enzymatic activities, and production of CLPs, Gl006 showed β-N-acetylglucosaminidase, chitobiosidase, total chitinase, β-1,3-glucanase, and protease activities. All the metabolites produced by the single strains were also found in the consortium, but in a culture medium dependent manner. The FA was found in the experiment on the interaction of the consortium with Foph Map5 in the minimal basal medium and in potato dextrose broth. The population of Foph was reduced by the consortium in vitro, under the synthetic media that favored the production of all the CWDE tested. In soil conditions, the consortium reduced the population of Foph by 63% in a synergistic way. Bs006 was recovered from the inner tissues of the plant, where Gl006 prevented the entry of Foph to the roots and reduced the incidence of the disease under the split root model. These results suggest that the consortium of Gl006 and Bs006 displays modes of action through CWDE and CLP´s and indirectly through induction of systemic resistance, which could act complementary since neither of them were enhanced in consortium. Here we characterized a consortium capable of reducing the population of Foph in soil and control the disease in a synergistic way.