Once you have cleaned the upholstery, spinkle baking soda on the dry upholstery and let it sit a few days. Then, when you can leave the car closed up for a day or two (especially if it will be sunny), pour some dry, unused coffee grounds into shallow dishes, and put them in the car, then close it up tightly; a day or two is great, if you can. Vacuum the baking soda, and let the car air out. Hopefully it will take care of it.
You might also check the pet store; they sell enzymatic products that you put on and let dry (like Febreeze), but that are specially formulated for pet urine.
I was told to try rubbing alcohol and water in a spray bottle. I mixed it strong and sprayed down the area and wiped up with rags. It's cheap and it works great. The alcohol kills the bacteria that causes the odor. Although I used it for dog odor it would be worth a try. (11/14/2009)
Natures Miracle for cats; the orange bottle, found at PetSmart and some other stores. Research this on-line. They have a wonderful site, with a site for discussions that are helpful. I have also had luck with Oxiclean on my indoor carpeting. (11/26/2009)