Surface-layer associated proteins (SLAP) of Lactobacillus paracasei ssp. paracasei M5-L and Lactobacillus casei Q8-L were examined to identify the functional basis for their protection within intestinal epithelial cells. The results showed that SLAP of M5-L and Q8-L remained active in a trypsin solution and retained a 45-kDa protein band, similar to that observed in controls. In contrast, under conditions of simulated gastric juice, the SLAP were partially degraded. Inhibitory effects of SLAP on adherence of Shigella sonnei to HT-29 cells were assessed with use of exclusion, competition, and replacement assays. In response to M5-L at 50 μg/mL SLAP, an inhibition ratio of 33% was obtained, while for Q8-L at 400 μg/mL SLAP, the inhibition ratio was 48%. Hoechst 33258 test results showed that cells infected with S. sonnei and co-incubated with SLAP of M5-L and Q8-L were only partially apoptotic, with apoptosis rates of 37.67 and 43.67%, respectively. These levels of apoptosis were substantially lower than that observed with cells infected with S. sonnei alone. In addition, the SLAP of Q8-L and M5-L reduced downstream caspase-1 activity and further modified apoptotic cell damage. Finally, SLAP of M5-L and Q8-L were also able to prevent S. sonnei-induced membrane damage by inhibiting delocalization of zonula occludens (ZO)-1 and reducing the amount of occludin produced by S. sonnei.