It means that he has done something wrong many times before but has not got in trouble for it. Now someone has caught him/ reprimanded him by saying "but he did this just once too often." It means that finally he will get into trouble or be punished. Example: A teenager steals lollies from a supermarket every time he goes there. One day he is caught and realizes that he "did this once too often".

= He has done it one time too many, and is now in trouble for it.