Soil salinity stress limits crop productivity by disrupting plant physiological processes, water uptake, creating ionic imbalance, and interrupting cellular homeostasis, causing oxidative damage. The present study investigates the potential of a habitat-adapted endophytic fungus, Fusarium isolates, to confer salinity stress tolerance in tomato. Amongst three isolates (K23, SF-5, and N-14) tested, symbiosis with SF-5 exhibited beneficial effects at early seedling growth under NaCl-induced stress. The beneficial effects of endophyte inoculation were maintained at the whole-plant level under greenhouse conditions subjected to 10 dS m⁻¹ salinity stress, with SF-5-inoculated plants exhibiting superior growth-related traits compared to uninoculated plants under the same stress conditions. Endophyte colonization significantly increased chlorophyll content and photosynthetic rate, reflecting enhanced photosynthetic efficiency under stress conditions. Histochemical analysis showed reduced accumulation of reactive oxygen species (O2⁻ and H2O2) and improved membrane stability in SF-5 inoculated stressed plants, suggesting enhanced antioxidant defense mechanisms. However, despite improvements in early vegetative and physiological processes, average fruit weight and total fruit yield did not show any improvement under high salinity in SF-5 inoculated plants. Fruit quality parameters showed differential responses, with reduced total soluble solids under stress. Overall, the results suggest that SF-5 confers salinity stress tolerance primarily by enhancing cellular tolerance via the alleviation of oxidative damage and the maintenance of higher photosynthetic efficiency. These findings demonstrate the potential of the fungal endophyte as a sustainable biological elicitor for enhancing resilience to salinity stress.