We isolated and examined two endophytic fungi for their potential to secrete phytohormones viz. gibberellins (GAs) and indoleacetic acid (IAA) and mitigate abiotic stresses like salinity and drought. The endophytic fungi Phoma glomerata LWL2 and Penicillium sp. LWL3 significantly promoted the shoot and allied growth attributes of GAs-deficient dwarf mutant Waito-C and Dongjin-beyo rice. Analysis of the pure cultures of these endophytic fungi showed biologically active GAs (GA1, GA3, GA4 and GA7) in various quantities. The cultures of P. glomerata and Penicillium sp. also contained IAA. The culture application and endophytic-association with host-cucumber plants significantly increased the plant biomass and related growth parameters under sodium chloride and polyethylene glycol induced salinity and drought stress as compared to control plants. The endophytic symbiosis resulted in significantly higher assimilation of essential nutrients like potassium, calcium and magnesium as compared to control plants during salinity stress. Endophytic-association reduced the sodium toxicity and promoted the host-benefit ratio in cucumber plants as compared to non-inoculated control plants. The symbiotic-association mitigated stress by compromising the activities of reduced glutathione, catalase, peroxidase and polyphenol oxidase. Under stress conditions, the endophyte-infection significantly modulated stress through down-regulated abscisic acid, altered jasmonic acid, and elevated salicylic acid contents as compared to control. In conclusion, the two endophytes significantly reprogrammed the growth of host plants during stress conditions.