Ingestion of milks fermented by Lactobacillus strains showing probiotic properties is an important tool to maintain gastrointestinal health. In this study, Lactobacillus rhamnosus D1 and Lactobacillus plantarum B7, isolated from Brazilian artisanal cheese, were used as starters for the functional fermented milks to assess their probiotic properties in a gnotobiotic animal model. Male germ-free Swiss mice received a single oral dose of milk fermented by each sample, and were challenged with Salmonella Typhimurium five days afterwards. Milk fermented by both Lactobacillus strains maintained counts above 10⁸ cfu/ml during cold storage. Lactobacillus strains colonised the gut of the germ-free-mice, maintaining their antagonistic effect. This colonisation led to a protective effect against Salmonella challenge, as demonstrated by reduced pathogen translocation and histological lesions, when compared to control group, especially for Lactobacillus rhamnosus D1. Additionally, mRNA expression of inflammatory (interferon gamma, interleukin (IL)-6, tumour necrosis factor alpha) and anti-inflammatory (transforming growth factor β1) cytokines was augmented in animals previously colonised and then challenged, when compared to other experimental groups. Lactobacillus plantarum B7 colonisation also promoted higher expression of IL-17, showing a proper maturation of colonised germ-free-mice immune system. IL-5 was stimulated by both strains’ colonisation and not by S. Typhimurium challenge.