We recently proposed the use of engineered irregularly shaped zinc oxide nanoparticles (ZnO NPs) coated with oleylamine (OAm), as photosynthetic biostimulants, to enhance crop yield. In the current research, we tested newly engineered rod-shaped ZnO nanorods (NRs) coated with oleylamine (ZnO@OAm NRs) regarding their in vivo behavior related to photosynthetic function and reactive oxygen species (ROS) generation in tomato (Lycopersicon esculentum Mill.) plants. ZnO@OAm NRs were produced via solvothermal synthesis. Their physicochemical assessment revealed a crystallite size of 15 nm, an organic coating of 8.7% w/w, a hydrodynamic diameter of 122 nm, and a ζ-potential of −4.8 mV. The chlorophyll content of tomato leaflets after a foliar spray with 15 mg L−1 ZnO@OAm NRs presented a hormetic response, with an increased content 30 min after the spray, which dropped to control levels 90 min after the spray. Simultaneously, 90 min after the spray, the efficiency of the oxygen-evolving complex (OEC) decreased significantly (p < 0.05) compared to control values, with a concomitant increase in ROS generation, a decrease in the maximum efficiency of PSII photochemistry (Fv/Fm), a decrease in the electron transport rate (ETR), and a decrease in the effective quantum yield of PSII photochemistry (ΦPSII), indicating reduced PSII efficiency. The decreased ETR and ΦPSII were due to the reduced efficiency of PSII reaction centers (Fv’/Fm’). There were no alterations in the excess excitation energy at PSII or the fraction of open PSII reaction centers (qp). We discovered that rod-shaped ZnO@OAm NRs reduced PSII photochemistry, in contrast to irregularly shaped ZnO@OAm NPs, which enhanced PSII efficiency. Thus, the shape and organic coating of the nanoparticles play a critical role in the mechanism of their action and their impact on crop yield when they are used in agriculture.