This study investigated the plant growth promotion and stress mitigation effects of Penicillium species RDA01, NICS01, and DFC01 on sesame (Sesamum indicum L.) plants. The fungal isolates NICS01 and DFC01 significantly enhanced shoot length, root length, and fresh and dry seedling weight, due to the secretion of various concentrations of amino acids (Asp, Thr, Ser, Asn, Glu, Gly, Ala, Val, Met, Ile, Leu, Tyr, Phe, Lys, His, Try, and Arg). Penicillium sp. NICS01 increased the amount of chlorophylls, proteins, amino acids, and lignans in the sesame plants more so than in controls. Sesame plant growth was stunted by high soil salinity, and application of the three fungal isolates increased plant survival. The RDA01 and NICS01 strains significantly increased shoot length and fresh and dry seedling weights under salt stress conditions. In addition, an in vitro study of the Penicillium spp. revealed their antagonistic activity toward the pathogenic fungi Fusarium spp. Fusarium spp. reduce shoot length; co-inoculation with the NICS01 or DFC01 isolates significantly increased shoot length in infected plants. Our results suggest that exogenous application of the Penicillium sp. NICS01 can act as a biofertilizer and a biocontrol agent to improve plant growth and enhance plant survival against salt stress and Fusarium infection.