Probiotic bacteria belonging to Lactobacillus spp. are important producers of bioactive molecules, known as postbiotics, that play essential roles in the immunological support of the intestinal mucosa. In this study, the system of co-culture of intestinal epithelial cells with macrophage cells in vitro was used to study the potential effect of postbiotic fractions of L. rhamonosus and L. plantarum on the modulation of the immune response induced by pro-inflammatory stimuli. This study’s results revealed that the presence of probiotic bacterial components on the mucosal surface in the early and late stage of inflammatory conditions is based on cellular interactions that control inflammation and consequent damage to the intestinal epithelium. In our studies, heat killed fractions of probiotic bacteria and their extracted proteins showed a beneficial effect on controlling inflammation, regardless of the strain tested, consequently protecting intestinal barrier damage. In conclusion, the presented results emphasize that the fractions of probiotic bacteria of L. plantarum and L. rhamnosus may play a significant role in the regulation of LPS-mediated cytotoxic activity in intestinal epithelial cells. The fractions of probiotic strains of L. rhamnosus and L. plantarum showed the potential to suppress inflammation, effectively activating the anti-inflammatory cytokine IL-10 and modulating the IL-18-related response.