There is a set of books titled Roster of Confederate Graves by the GA Division UDC that may possibly help you locate your ancestor's grave. This set of books lists the names and locations of all the graves of known Confederate soldiers/veterans (from GA and all other states) buried in GA. Additionly, it lists the names and locations of all of the graves of known Confederate soldiers/veterans from GA buried in other states. Unfortunately, these books aren't 100% complete and the info in them isn't 100% accurate, but they are certainly worth looking at. Some larger libraries with a good genealogy collection have them. I know for sure that the main Atlanta Library has a set and if you call them, maybe they would check the index for you ancestor's name. If you go to http://www.worldcat.org/
and do a search for this set of books, you can find other libraries to contact about checking for you ancestor’s grave location. Good Luck!