The utilization of symbiosis with beneficial microorganisms provides a strategy to alleviate salt stress that reduces existing gaps in crops production. The root endophytic fungus Piriformospora indica has shown to improve plant growth in diverse plant species under biotic stress, while limited reports have discussed the interaction of P. indica with tomato under salt stress. In this study, the impact of P. indica on tomato exposed to 200 mM NaCl for one month in soil-free culture was examined. Growth performance, marker osmolytes, antioxidant enzymes and expression of LeNHX1-4 genes of tomato leaves were measured. Results show that colonization of roots by P. indica improved root branching, fresh and dry weight of salt-stressed plants. Likewise, P. indica colonization increased levels of chlorophyll b, indole acetic acid, catalase and superoxide dismutase in leaves of tomato under salt stress. Meanwhile, P. indica reduced the increase of abscisic acid and proline levels when compared to non-colonized plants. Importantly, Na+/K+ ratios in shoots and roots of colonized plants were lower than in the corresponding non-colonized plants, which may be attributed to the higher K+ concentration observed in leaves and roots of colonized plants under saline water irrigation condition. This change in ion homeostasis was combined with an increase in LeNHX1 transcripts in leaves of colonized plants. Moreover, compared to non-treated plants, colonization with P. indica enhanced fruit yield by 22% and 65% under normal and saline water irrigation, respectively. Our study shows that P. indica enhances the growth and yield of tomato plants under normal and salt stress conditions, opening up a window of opportunity for its application in desert agriculture.