In tomato culture, low-node-order pinching system at high planting density, combined with an increased number of cropping times per year and an extended nursery period, are important for obtaining high yields. The production of flowering transplants that are as advanced as possible by the time of transplanting is necessary because of the limited area available in the nursery, and it is important to control excessive stem elongation of transplants during this stage. The height of seedlings increased more during the day than at night, and this stem elongation was correlated with elongation of epidermal cells. As seedlings were grown by quantitative nutrient management and stopping the nutrient supply at night during this stage could decrease plant heights compared with the heights of seedlings grown in an electric conductivity-based control using a root-zone limiting hydroponic system. The dry matter ratio and root: shoot ratio of the transplants grown with quantitative nutrient management and without supplying nutrient solution at night were both higher than those in the control. After transplanting into an NFT system, there was no significant difference in the yields of transplants grown among under those treatments. Based on these results, we propose using an approach based on quantitative nutrient control and suspension of nutrient supply at night in order to control excessive stem elongation during subsequent nursery stages.