A control system of a vehicle including an engine and an automatic transmission operable to form one of a plurality of gear positions set according to running conditions of the vehicle, and a method of controlling the vehicle are provided. In the control, the rotational speed of an input-side rotary shaft of a shifting mechanism of the transmission is detected, and the vehicle is controlled so that, when an execution condition that one of the gear positions set according to the running conditions is maintained and the rotational speed of the input-side rotary shaft has increased to be higher than a rotational speed corresponding to the set gear position is satisfied, the vehicle is brought into running conditions that will eliminate a state in which air is present in the hydraulic fluid supplied from an oil supply device.