The production and quality of tomato seedlings needs many growth factors and production requirements besides controlling the phytopathogens. Paclobutrazol (PBZ) has benefit applications in improving crop productivity under biotic stress (Alternaria solani, the causal agent of early blight disease in tomatoes). In the current study, the foliar application of PBZ, at rates of 25, 50, and 100 mg L−1, was evaluated against early blight disease in tomatoes under greenhouse conditions. The roles of PBZ to extend tomato seedling lives and handling in nurseries were also investigated by measuring different the biochemical (leaf enzymes, including catalase and peroxidase) and histological attributes of tomato seedlings. Disease assessment confirmed that PBZ enhanced the quality of tomato seedlings and induced resistance to early blight disease post inoculation, at 7, 14, and 21 days. Higher values in chlorophyll content, enzyme activities, and anatomical features of stem (cuticle thickness) and stomata (numbers and thickness) were recorded, due to applied PBZ. This may support the delay of the transplanting of tomato seedlings without damage. The reason for this extending tomato seedling life may be due to the role of PBZ treatment in producing seedlings to be greener, more compact, and have a better root system. The most obvious finding to emerge from this study is that PBZ has a distinguished impact in ameliorating biotic stress, especially of the early blight disease under greenhouse conditions. Further studies, which consider molecular variables, will be conducted to explore the role of PBZ in more detail.