Plant virus infection has a negative impact on agricultural crops. One of the main problems is controlling viral diseases, as the only option is to prevent plant–virus interactions. Some studies have focused on the application of nanoparticles (NPs) to combat plant pathogens, but their use against viral diseases is still underexplored. Moreover, the antiviral mechanisms of NPs are not fully understood, and more studies are needed to provide evidence of the mechanisms involved. This study assessed the comparison between innovative Ti-NPs derived from Ti-MOF material and Ag-NPs in their effects on potato virus Y (PVYNTN) - tobacco “Samsun” interaction. The results clearly indicated that foliar pretreatment with 25 and 50 ppm of Ti-NPs and Ag-NPs significantly reduced PVYNTN concentration without toxic effect on plants. Interestingly, SEM (Scanning Electron Microscope) and LIBS (Laser Induced Breakdown Spectroscopy) analyses confirmed a lower concentration of Ti-NPs compared with Ag-NPs, but Ti-NPs migrated more intensively than Ag-NPs in tobacco tissues. Moreover, the smaller size of Ti-NPs (14–19 nm) revealed a stronger preventive antiviral effect, expressed in tobacco cells by a significant reduction of PVYNTN-CP gene expression and the absence of viral cytoplasmic inclusions between 7 and 21 dpi (day post inoculation). Additionally, it was demonstrated that only Ti-NPs had direct contact with PVYNTN in in vitro test resulting in virus particles fragmentation. Furthermore, it was revealed that virus limitation as an effect of Ti-NPs and Ag-NPs application, along with significant induction of total soluble phenolic compounds and proline content, was accompanied by reduced lipid peroxidation levels compared with PVYNTN-inoculated and mock-inoculated tobacco plants without pretreatment. Additionally, PVYNTN-infected tobacco pretreated with Ti-NPs and Ag-NPs displayed a highly dynamic increase in salicylic acid, which plays a role in systemic resistance as a signaling factor. This study also reported that SOD (superoxide dismutase), PAL (phenylalanine ammonia-lyase), and PPO (polyphenol oxidase) are important components of the antioxidant response to Ti-NPs and Ag-NPs application, leading to PVYNTN suppression. Correspondingly, the significant increase in SA (salicylic acid) was followed by upregulation of NtPR-5 and NtPR-12 genes, with slight induction of NtPR-1 compared with mock-inoculated plants with and without Ti-NP and Ag-NP pretreatment, in contrast to the downregulation of NtPR-2 in comparison with mock-inoculated and virus-inoculated plants. Overall, this study established that Ti-NPs from Ti-MOF (metal–organic frameworks) and Ag-NP pretreatments offer a promising preventive approach in the PVYNTN-tobacco pathosystem without phytotoxicity risk. Nonetheless, future research is needed for deeper analyses of the mechanisms of Ti-NP and Ag-NP action, particularly focusing on their interactions with viral particles and plants.