Buy the dealer paint and clear. Be thorough about cleaning areas to be painted.
Apply with toothpick one layer at a time fill the pit slowly. Let each dry completely. Hands steady.
After applying & drying clearcoat layer sand with 600 wet/dry light pressure. You'll get a great blend and after waxing you'll have trouble finding the spots again.

 

Ive heard people on here recommend paintscratch.com just make sure you get your color code from the trunk sticker next to the spare tire