Bacterial wilt disease caused by Ralstonia solanacearum affects a wide variety of crops, including tomatoes. Novel natural products and organisms offer opportunities for innovation in agroindustry as an alternative way to pest and pathogen controls. Gluconacetobacter diazotrophicus Pal5 (Gd) belongs to PGPBEs (Plant-Growth-Promoting Bacterial Endophytes), which facilitate plant growth via phytostimulation, biofertilization and biocontrol. In this study Rio Grande tomato seedlings were inoculated with Gd to test its ability to colonize them and its protective potential against the phytopathogen Ralstonia solanacearum A21 (Rso). Gd root and stem colonization of tomato seedlings were determined. Stem height was markedly affected by the inoculation with Gd after 80 dpi and a set of biochemical and anatomical structural changes in root, stem and leaves were triggered. The resistance mechanisms elicited in the plant after inoculation with the endophytic bacteria involved reinforcement of the cell walls in the root vascular cylinder and stem vascular bundles, with the presence of an augmented number of contact cells with dense cellular content, probably pectins, lignin and tannins. Roots and stems presented thicker and more lignified xylem vessel walls. These plants showed statistically significant differences with mock inoculated plants in several quantitative variables, such as area of the xylem vessels in root and stem. Biocontrol assays without Gd showed wilting at 9 dpi with Rso. Histological analysis showed bacteria cells filled xylem vessels and dispersal through tissue degradation. In contrast, plants with Gd remained asymptomatic and phytopathogen colonization was observed to a lesser extent in the stem and root. Anatomical changes primed by Gd were enhanced upon Rso infection and the tyloses process appeared. Therefore, Gd primes the resistance mechanism in Rio Grande tomato plants significantly reducing bacterial wilt caused by Rso.