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The present study was undertaken to explore acidotolerant rhizobial and non-rhizobial bacteria associated with root nodules of soybean (Glycine max L.). Genotypic and phenotypic characterization regarding nitrogen fixation, nodulation and other potentially plant growth-promotion traits were performed in several isolates. Influences of bacterial inoculation on symbiotic nitrogen fixation and soybean growth were evaluated through flask and pot experiments in a greenhouse. The highest nitrogen-fixing activity was recorded in isolate Bra6, which was closely related to Bradyrhizobium diazoefficiens based on 16S rDNA, nifH, and nodD gene sequences. All the non-rhizobial Pseudomonas isolates possessed multiple plant growth-promoting traits, with various hydrolytic patterns toward plant constituents. In sterile water agar-containing flasks, Bra6 + Pse2 treatment significantly (p < 0.05) increased the number of nodules, fresh weight, and dry weight of both root and shoot. This also led to the increment of most of the nutrients in the soybean plant compared with the uninoculated control or sole inoculation of Bra6. In non-sterile strongly acidic soil-containing pots, co-inoculation with Bra6 and various Pseudomonas isolates showed distinctively positive effects on symbiotic nitrogen fixation and soybean growth. The highest symbiotic nitrogen-fixing activity; root and shoot biomass; as well as N, P, K, Ca, Mg, S, Mn, Cu, and Zn contents of soybean plant were observed in Bra6 + Pse2 treatment. Synergistic symbiosis occurred through co-inoculation with Bradyrhizobium and Pseudomonas isolates, which further enhanced nutrients’ acquisition and growth of soybean in the strongly acidic soils.