I've seen that story several times and the evidence for it is very thin. From the sources I've read the first time it appeared was in 1905 in an issue of confederate veteran. That story has a different take on it though.
NEGRO COMMUNED AT ST. PAUL'S CHURCH," CONFEDERATE VETERAN, 13 (AUGUST 1905): 360. "Col. T. L. Broun, of Charleston, W. Va., writes of having been present at St. Paul's Church, Richmond, Va., just after the war when a negro marched to the communion table ahead of the congregation. His account of the event is as follows:
"Two months after the evacuation of Richmond business called me to Richmond for a few days, and on a Sunday morning in June, 1865, I attended St. Paul's Church. Dr. Minnegerode [sic] preached. It was communion day; and when the minister was ready to administer the holy communion, a negro in the church arose and advanced to the communion table. He was tall, well-dressed, and black. This was a great surprise and shock to the communicants and others present. Its effect upon the communicants was startling, and for several moments they retained their seats in solemn silence and did not move, being deeply chagrined at this attempt to inaugurate the "new regime" to offend and humiliate them during their most devoted Church services. Dr. Minnegerode [sic] was evidently embarrassed.
General Robert E. Lee was present, and, ignoring the action and presence of the negro, arose in his usual dignified and self-possessed manner, walked up the aisle to the chancel rail, and reverently knelt down to partake of the communion, and not far from the negro. This lofty conception of duty by Gen. Lee under such provoking and irritating circumstances had a magic effect upon the other communicants (including the writer), who went forward to the communion table.
By this action of Gen. Lee the services were conducted as if the negro had not been present. It was a grand exhibition of superiority shown by a true Christian and great soldier under the most trying and offensive circumstances."
I find it hard to believe a black man would have even been allowed in a white church in Virginia in 1865. I think the whole story is very suspect.