Multiple ways you could approach this. I would use a scratch pen to remove the rust down to the metal, apply primer and top coat. I’d use a small brush or dabber to apply the primer and paint. If you’re really particular, you can feather the edges and wet sand to blend the edges. If you’re really, really particular, take care of the rust and have a pro airbrush the spot for a close match. Your local car dealer has a vendor that comes by to do this on a regular basis.

Others will likely recommend a chemical like Evaporust to mitigate the rust first. Nothing wrong with this although you’ll need to get creative with how to seal the chemical so it can work.