Just to set one point straight, your employer should have no issue with you and this incident, you weren't smoking in the vehicle and the vehicle is just being used as a means of identifying you so unless there is a clause in your contract of employment for non-littering in public places or one that completely bans you from smoking anywhere then they have no complaint and probably wouldn't even have discussed it with you.
What would have happened had you not identified yourself is that eventually your employer would have received a letter informing them that a user of their vehicle was witnessed committing an offence, details of which would have been described, and your employer would be asked to identify the employee on that date.
Exactly the same thing happened to me some years ago when one of my employees was spotted flicking a cigarette out of one of my vans when driving, I dobbed him in of course.