What to do if my uncle passed away with a notarized Will but his son is now trying to take a vehicle that was left to his girlfriend at the time of his passing?

Your uncle's son does not have the right to take your uncle's vehicle unless he is on the title to the vehicle.  Florida, and most states, have laws that make it easy to transfer title to a vehicle according to a will. 

I suggest you or the girlfriend call the department of motor vehicles and ask how this is done.  They usually know how to do it or can send you to the authority who knows how to do it.  I also suggest you tell the son you will call the police if he attempts to take a vehicle that is not his.