Vegetable crops such as tomato are highly susceptible to various pathogens. Nanoparticles (NPs) are emerging as effective nano-bactericides for managing plant pathogens. Communities of rhizosphere bacteria are essential for plant physiological health and also serve as a critical factor in evaluating the environmental compatibility of NPs. We evaluated the effects of a nano-bactericide (Cu-Ag nanoparticles) and a commercial bactericide (thiodiazole–copper) on the rhizosphere microbiome of tomato. The results show that low and high doses of the two bactericides induced alterations in the bacterial community structure to differing extents. Cu-Ag nanoparticles increased the relative abundance of potentially beneficial bacteria, including Bacteroidota, Gemmatimonadota, Acidobacteriota, and Actinobacteriota. Functional prediction revealed that Cu-Ag nanoparticles may affect the metabolic pathways of tomato root rhizosphere microorganisms and regulate the lacI/galR family, which controls virulence factors and bacterial metabolism. This study provides insight into the influence of metal nanoparticles on plant rhizosphere microbiomes and may lay a foundation for the application of nano-bactericides for the environmentally friendly control of plant diseases.