Centre of mass of a system cannot change its state of motion, unless there is an external force acting on it. Yet the internal force of brakes can bring a car to rest. Then what stops the car?
Friction. The wheels are one system, the brakes are another. Relative motion between the wheels and the brakes is what causes friction, and this reduces the angular speed of the wheels. A reduction in the angular speed of the wheels requires the car to slow down too, assuming the wheels don't slip.