Dear

    You need to understand wht is your system, broadly we can devide your car to two systems your tyre and the body of the car both connected by some mechanical interface so when you apply brake its external to the tyre so its starts stopping and at the interface a newtonian third law force pair comes in to play one force of which stops the body of the car .

 

Now when we apply brake the decelerating tyre experiences an extenal force due to friction which adjusts itself its magnitude and direction to confirm rolling

which deccelerates the COM of the car