A system for protecting a vehicle inverter from overvoltage includes a first inverter having switching elements and converting energy from an energy storage device into AC power. A first motor is driven by receiving the converted AC power. A second inverter is connected in parallel with the first inverter, includes a switching elements, and converts energy from the energy storage device into AC power. A second motor is driven by receiving the converted AC power. A first capacitor is connected in parallel between the first inverter and the energy storage device and stores electric energy of the first motor during regenerative braking. A controller turns off a relay connecting the energy storage device and the motor when a voltage of the first capacitor is equal to or greater than a predetermined voltage and operates the switching elements in the inverters in response to first and second current commands.