Microgrid systems are built to integrate a generation mix of solar and wind renewable energy resources that are generally intermittent in nature. This paper presents a novel decentralized multi-agent system to securely operate microgrids in real-time while maintaining generation, load balance. Agents provide a normal operation in a grid-connected mode and a contingency operation in an islanded mode for fault handling. Fault handling is especially critical in microgrid operation to simulate possible contingencies and microgrid outages in a real-world scenario. A robust agent design has been implemented using MATLAB-Simulink and Java Agent Development Framework technologies to simulate microgrids with load management and distributed generators control. The microgrid of the German Jordanian University has been used for simulation for Summer and Winter photovoltaic generation and load profiles. The results show agent capabilities to operate microgrid in real-time and its ability to coordinate and adjust generation and load. In a simulated fault incident, agents coordinate and adjust to a normal operation in 0.012 seconds, a negligible time for microgrid restoration. This clearly shows that the multi-agent system is a viable solution to operate MG in real-time.