Water deficit can alter plant growth and stress-related biochemical and molecular responses. Four fungal isolates obtained from Pinus cembroides roots—Cadophora sp., Phialophora livistonae, Pochonia sp., and Pochonia chlamydosporia—were evaluated in vitro under increasing polyethylene glycol (PEG-6000) concentrations. Pochonia sp. and P. livistonae were subsequently selected for inoculation of tomato seedlings grown at 100, 75, 50, or 25% of substrate water-holding capacity. Seedling growth, root and leaf biochemical traits, antioxidant enzyme activities, and expression of five water-deficit-associated genes were evaluated using factorial analyses. Pochonia sp. maintained the greatest colony diameter across the PEG-6000 treatments, while Pochonia sp. and P. livistonae produced the highest fresh fungal biomass at 20% PEG-6000. Irrigation level significantly influenced most seedling growth traits. Fungal inoculation significantly affected root fresh and dry weights overall, but within level comparisons identified a higher root fresh weight with P. livistonae than in uninoculated seedlings only under mild water stress (75%). Under the same conditions, P. livistonae reduced root proline content relative to the uninoculated control and Pochonia sp. Root catalase activity showed a significant inoculation × irrigation inter-action, whereas total phenolic content and leaf antioxidant enzyme activities showed no significant treatment effects. Irrigation significantly affected Fe-SOD gene expression, but fungal inoculation had no significant effect on any evaluated gene; none of the planned inoculation contrasts remained significant after Holm adjustment. These findings indicate selective, mainly root-associated responses to fungal inoculation rather than consistent enhancement of tomato growth or water-deficit tolerance. Further work should verify fungal colonization and assess plant water status and performance under production conditions.