Due to the higher potential for enhancing nutrient use efficiency, nanofertilizer (NF) is crucial in sustainable crop production. Thus, foliar-applied mixed nanofertilizer (MNFf) and commercial fertilizer (CF) into the soil (CFs) were claimed together ([MNFf + CFs]) and comparative nutrient use efficiency (NUE), productivity, and nutritional properties of tomato fruits were investigated. The mixed nanofertilizer (MNF) was prepared in our laboratory and characterized using scanning electron microscopy, X-ray diffraction, and Fourier transform infrared. To avoid the interference of other factors, all the treatments were divided into three groups: (i) blank treatment (no fertilizer), (ii) CF treatment, and (iii) combined [MNFf + CFs] treatment. The vegetative growth and qualitative and quantitative attributes of tomatoes were recorded, and the NUE, total production, and benefit–cost ratio (BCR) were also calculated. In addition, comparative nutritional properties for all treatments were analyzed. The plant’s height, stem diameter, root length, photosynthetic pigments, leaf minerals, and qualitative traits of tomato fruits were significantly (p < 0.05) increased by [MNFf + CFs] treatment compared to CFs. The protein, fiber, Fe, Zn, and K contents were significantly (p < 0.05) increased by 23.80, 38.10, 44.23, 60.01, and 2.39%, respectively, with the [MNFf + CFs] treatment as compared to CFs, while the ash and protein contents were both lower than the untreated tomato. Moreover, [MNFf + CFs] treatment has significantly (p < 0.05) increased the antioxidant properties. The NUE, total production, and BCR were also increased by 26.08, 26.04, and 25.38%, respectively, with the same treatment. Thus, [MNFf + CFs] treatment could be a potential alternative for reducing the excess use of CF.