Aspergillus flavus infection of vegetative tissues can affect the development and integrity of the plant and poses dangerous risks on human and animal health. Thus, safe and easily applied approaches are employed to inhibit A. flavus growth. To this end, the fungal endophyte, i.e., Aspergillus fumigatus, was used as a safe biocontrol agent to reduce the growth of A. flavus and its infection in maize seedlings. Interestingly, the safe endophytic A. fumigatus exhibited antifungal activity (e.g., 77% of growth inhibition) against A. flavus. It also reduced the creation of aflatoxins, particularly aflatoxin B1 (AFB1, 90.9%). At plant level, maize seedling growth, leaves and root anatomy and the changes in redox status were estimated. Infected seeds treated with A. fumigatus significantly improved the germination rate by 88.53%. The ultrastructure of the infected leaves showed severe disturbances in the internal structures, such as lack of differentiation in cells, cracking, and lysis in the cell wall and destruction in the nucleus semi-lysis of chloroplasts. Ultrastructure observations indicated that A. fumigatus treatment increased maize (leaf and root) cell wall thickness that consequentially reduced the invasion of the pathogenic A. flavus. It was also interesting that the infected seedlings recovered after being treated with A. fumigatus, as it was observed in growth characteristics and photosynthetic pigments. Moreover, infected maize plants showed increased oxidative stress (lipid peroxidation and H2O2), which was significantly mitigated by A. fumigatus treatment. This mitigation was at least partially explained by inducing the antioxidant defense system, i.e., increased phenols and proline levels (23.3 and 31.17%, respectively) and POD, PPO, SOD and CAT enzymes activity (29.50, 57.58, 32.14 and 29.52%, respectively). Overall, our study suggests that endophytic A. fumigatus treatment could be commercially used for the safe control of aflatoxins production and for inducing biotic stress tolerance of A. flavus-infected maize plants.