Vulvovaginal candidiasis is the second most common vaginal infection caused by drug-resistant Candida species that affects about 70-75% of reproductive age group women across the globe. As current-day antifungal drugs are ineffective against the biofilms formed by the drug-resistant Candida strains, several natural compounds and antagonistic microbes are being explored as alternative antifungal agents. In the present study, we investigated the anti-biofilm activity of Cell-Free Supernatant (CFS) extracted from the commercially available probiotics VSL-3 against the biofilms of Candida species and also evaluated their efficacy in curbing the yeast-to-hyphal transition. Various methodologies like crystal violet staining and scanning electron microscopy were used to study the effect of CFS against the biofilms formed by the species. The ability of CFS to interfere with yeast to hyphal transition in Candida was studied by colony morphology assay and visually confirmed with phase contrast microscopy. The potential of the CFS of the probiotics was also evaluated using goat buccal tissue, a novel ex-vivo model that mimics the vaginal environment. Moreover, the supernatant extracted from VSL-3 had the ability to down-regulate the expression of virulence genes of Candida from the biofilm formed over the ex-vivo model. These results emphasize the anti-fungal and anti-infective properties of the CFS of VSL-3 against drug-resistant Candida strains causing vulvovaginal candidiasis.