Tobacco mildew is a common fungal disease that reduces tobacco quality, resulting in serious economic losses in the tobacco industry. In this study, the pathogens Aspergillus niger, Aspergillus flavus, and Rhizopus arrhizus were isolated from infected leaves. Furthermore, five plant endophytic bacteria isolated from healthy tobacco leaves were found to possess strong antifungal activity against these pathogens. Among these strains, Bacillus amyloliquefaciens ZH-2 exerted the strongest antagonistic effect against all mildew types (bacteriosphere diameter >
22 mm). The antagonistic action of ZH-2 was further observed using scanning electron microscopy, which revealed signs of contraction, deformation, and dissolution of the treated mycelia compared with that seen in the control group. The ZH-2 strain was found to produce high levels of proteases, chitinases, and β-1,3-glucanase, contributing to its antifungal activity via fungal cell wall rupture. The antifungal activity of ZH-2 was also demonstrated in the application test, as indicated by the significant reduction in mildew disease severity in tobacco leaves treated with this strain. Fermentation tests showed that the quality of ZH-2-treated, solid-state fermented tobacco leaves was superior to that of the control. Specifically, the alkaloid content significantly decreased by 10.62%, whereas the total and reduced sugar contents increased by 12.9 and 55.75%, respectively. Furthermore, macromolecular starch, cellulose, and protein contents significantly decreased by 25.85, 12.77, and 10.04%, respectively. These results indicate that the Bacillus amyloliquefaciens ZH-2 strain is effective against tobacco mildew and can improve tobacco quality upon solid-state fermentation.