
Sounds like eh gets stressed when you leave him in the car and is telling you off for leaving him. My Jozi does this to me if I leave someone else holding her lead while I pop to the loo or into a shop.
Off the top of my head I would practise not getting into the car until he stops. approach the car and tell him quiet (assuming he knows what that means), do not get into the car or open the door until he stops for a moment. If he starts again close the door or get back out. Same principole as not letting a dog that barks with anticipation of arriving in the park, where it woudln't be let out until it was silent.
Silence equals you sitting in the car with him, barking mens you stay outside.
Also does he so this if one of you stays in the car with him.
As a short term measure it might be better for you to take turns with your toilet breaks if he is quiet when not left alone.