Black mold and green mold caused by Alternaria alternata and Penicillium digitatum, respectively, are the most important decay pathogens of tomato fruits during storage. Our research was aimed to control tomato phytopathogenic fungi A. alternata and P. digitatum in vitro and in vivo by using natural nanomaterials rosmarinic acid (RA-NPs) at concentrations of 0.3 and 0.6 mM, glycyrrhizic acid (GA-NPs) and glycyrrhizic acid ammounium salt (GAS-NPs) (0.1–0.2 mM). Characterizations of the tested nanoparticles were carried out by using dynamic light scattering which revealed that synthesized nanoparticles had particle sizes of less than 100 nm. In vitro studies revealed that the three tested nanoparticles reduced the growth of A. alternata and P. digitatum. Glycyrrhizic acid nanoparticles were the most effective in reducing the growth of the two tested pathogens followed by RA-NPs at 0.6 mM. Observations of A. alternata and P. digitatum by scanning electron microscopy (SEM) showed severe damage in the hyphae and deformities in the conidia due to the effect of the tested nanoparticles. In vivo results showed that, dipping tomato fruits as a post-harvest treatment in all of the tested nanoparticles at different concentrations, then stored at 10 ± 1°C and 90–95% relative humidity (RH) for 20 days greatly reduced the disease severity of infected fruits with the two tested pathogens. GA-NPs at 0.2 mM significantly reduced the development of black mold rot on tomato fruits. RA-NPs at 0.6 mM had the best effect in controlling P. digitatum of all naturally and artificially inoculated tomato fruits. Also, individual treatments of tomato fruits with RA-NPs, GA-NPs and GAS-NPs significantly reduced postharvest losses of fruit since they delayed decay and maintained fruit quality characteristics such as fruit firmness, titratable acidity and total soluble solids during cold storage.