Avoid the sharpie. They leave a purple-ish reflection under certain lighting conditions. I recommend using some gloss black acrylic paint. It's cheap, will stay a little flexible, and will blend in pretty well. Use a tiny brush or a toothpick to apply. Cover the smallest area possible to make the repair. The larger area you paint, the more noticeable it will be.
There are products that are used to fill leather damage, but I have no experience with them. I have a feeling they'll be too thick, and may done more harm than good (odd texture) in this case.