Ralstonia solanacearum causes bacterial wilt and undergoes spontaneous phenotypic conversion (PC) from its wild-type to an avirulent form. In previous studies, we reported that pre-inoculation of plants with PC mutants suppressed bacterial wilt and Verticillium wilt in eggplants. In addition, we previously revealed bacterial differences in the control effects in eggplant among PC mutants; 8107PC and 8103PC were selected as effective strains for controlling Verticillium wilt and bacterial wilt diseases, respectively. In this study, we investigated the biological control efficiencies of 8107PC inoculation among 19 eggplant cultivars, including 13 commercial cultivars and six rootstock cultivars, to select eggplant cultivars that stably prevent Verticillium wilt using PC mutants. Varietal differences in biological control were confirmed. Additionally, cultivars with a higher potential resistance to Verticillium wilt tended to be more suppressed by the PC mutant, suggesting that cultivar selection is important to achieve effective biocontrol. Furthermore, we found that the biocontrol with 8107PC against Verticillium wilt in grafted eggplant seedlings of Solanum melongena ‘Senryo nigo’ onto S. torvum ‘Tonashimu’ was the most effective rootstock cultivar against Verticillium wilt. The biocontrol was more effective than the non-grafted seedlings inoculated with the PC mutant and the grated seedlings not inoculated with the PC mutant. We also investigated biocontrol by the 8103PC inoculation against bacterial wilt using grafted seedlings (‘Senryo nigo’ as the scion) with ‘Tonashimu’ or S. melongena ‘Daitaro’ as rootstocks. Although ‘Daitaro’ had a low control effect against Verticillium wilt, the grafted seedlings showed a high control effect against bacterial wilt, regardless of the PC mutant inoculation. Conversely, seedlings grafted with ‘Tonashimu’ were vulnerable to bacterial wilt; however, inoculation with the PC mutant completely suppressed the disease. Therefore, this study demonstrated that bacterial wilt and Verticillium wilt could be effectively controlled by inoculation with PC mutants in seedlings grafted with ‘Tonashimu’. The combination of grafting and PC mutant inoculation is expected to be effective for the combined control of Verticillium wilt and bacterial wilt diseases in eggplants.