We investigated the mechanism by which Salmonella inhibits transport to lysosomes to survive in macrophages. We have purified the Salmonella-containing phagosomes from macrophages and determined the presence of different endocytic Rab proteins on the phagosomes. Our results have shown that live Salmonella-containing phagosomes recruit more Rab5 than dead Salmonella-containing phagosomes. Recruitment of Rab5 on live Salmonella-containing phagosomes depends on the presence of viable bacteria in the phagosomes. Subsequently, we identified an effector molecule of Salmonella, SopE, which specifically binds Rab5. Moreover, SopE is found to be a specific nucleotide exchange factor for Rab5 and thereby retains Rab5 in an active conformation. Activated Rab5 on Salmonella-containing phagosomes promotes fusion with early endosomes and thus avoids transport to the lysosomes.