This is an unusual situation. Ordinarily burials at a Confederate hospital are unmarked, or marked simply "unknown." Sometimes the location of a cemetery within a growing town has been forgotten and burial sites paved over. However, a cemetery record book kept at the University of Virginia survived the war. In addition, just after the war Charlottesville citizens raised money to replace wooden markers. I don't know of another case like this.

Findagrave has an index of all interments.
http://www.findagrave.com/cgi-bin/fg.cgi?page=cr&CRid=2132655

Here's an article about the wartime cemetery at the University of Virginia -
http://www2.dailyprogress.com/lifestyles/2012/may/20/yesteryears-uvas-confederate-cemetery-ar-1925738/