As an effective alternative to traditional pesticides, ozonated water has been used for direct immersion and spraying applications, respectively, against the pathogenic bacterium Ralstonia solanacearum (R. solanacearum) and fungus Alternaria solani (A. solani) that are pathogens of tomato. Immersing R. solanacearum in 0.8 mg/L ozonated water resulted in complete inactivation, while the growth-inhibition rates of the A. solani radial mycelia gradually increased with a 67.0% decrease compared to those of the control at an ozonated water concentration of 7.5 mg/L. This indicated that ozonated water was effective at restraining pathogens in the tomato plant. In addition, spraying wild tomato species (Solanum lycopersicum) plants with ozonated water at concentrations below 10 mg/L for 25 d had no negative effects after treatment compared to those of the control. Photosynthetic activities and the antioxidant system response in the untreated and ozonated water-treated plant leaves had no observable changes. To determine the optimal ozonated water concentration for the pathogen and its host plant, we examined a variety of modes of action, and then, below 10 mg/L of ozonated water. Thus, ozonated water not only inhibits the proliferation of plant pathogens, but is an effective alternative to the pesticides traditionally used to prevent disease in agricultural production.