I would clean the spot with CLR or some other type of rust remover. Apply a thin coat of touch up paint normally to the spot. Let it dry for a half hour. Then, come back and put a heavy coat to build it up. It doesn't matter how it looks at this point. You just need a buildup. Let dry another half hour. Put some water in a spray bottle and mist the spot on the car, then soak a 1000 grit sand paper with the water. Gently, very gently massage the spot and just lightly skate across the paint buildup until it looks perfect. Apply a clearcoat. Done.
Alternatively, you can get something like the Quixx scratch remover system from most auto parts stores. Instead of wet sanding, you can do the buildup as described above, but then use the Quixx buffer pads on a drill with their provided rubbing and polishing compounds to do the blend. The sandpaper method is quicker and easier though, as buffing can beat off the paint you put on if not careful.
Alternatively, you can get something like the Quixx scratch remover system from most auto parts stores. Instead of wet sanding, you can do the buildup as described above, but then use the Quixx buffer pads on a drill with their provided rubbing and polishing compounds to do the blend. The sandpaper method is quicker and easier though, as buffing can beat off the paint you put on if not careful.