Water deficit (WD) promotes great losses in agriculture, and the development of new sustainable technologies to mitigate the effects of this stress on plants is essential. This study aimed to evaluate the morphophysiological and biochemical alterations induced by the priming of tomato seeds with different formulations in plants under field capacity and WD conditions. In the first experiment, the treatments consisted of nanoparticles of alginate/chitosan and chitosan/tripolyphosphate containing gibberellic acid (GA3) in different concentrations (0.5, 5, and 50 µg mL−1 GA3), in addition to control with deionized water. The alginate/chitosan (5 µg mL−1 GA3) provided the greatest gains in plant growth under field capacity. In addition, under WD this treatment reduced damage to photosystem II (−14%), stomatal conductance (−13%), and water loss (−38%) and increased the instantaneous carboxylation efficiency (+24%) and intrinsic water use efficiency (+12%). In the second experiment, the treatments were alginate/chitosan nanoparticles containing GA3 (NPGA3 5 µg mL−1), free GA3 (GA3 5 µg mL−1), nanoparticles without GA3 (NP), deionized water (WATER), and non-primed seeds (CONT). Under WD, GA3 and CONT maintained plant growth and lost water rapidly, reducing stomatal conductance (−87%) and net photosynthesis (−69%). In contrast, NPGA3 decreased leaf area (−44%) and increased root-to-shoot ratio (+39%) when compared to GA3, reducing water loss (−28%). Activation of protective mechanisms (e.g., superoxide dismutase and catalase activities) by WATER, NPGA3, and NP treatments also resulted in lower susceptibility to WD compared to CONT and GA3. The results highlight the positive effect of seed priming on plant response to WD, which was enhanced by the use of nanoencapsulated GA3.