McDonnell became the first governor since 2001 to designate April to commemorate the secessionist, slaveholding South.
The last governor to do that was fellow Republican Jim Gilmore. Since then, Democrats Mark Warner and Tim Kaine refused to issue the proclamation.
Warner, in his first year as governor in 2002, discontinued the proclamation sought each spring by the Sons of Confederate Veterans. Before that, the proclamations were met annually with denunciations from black groups.
McDonnell's initial decision not to mention slavery in the proclamation drew sharp criticism.
Black members of the General Assembly, all Democrats, said McDonnell's proclamation was "offensive and offered a disturbing revision of the Civil War and the brutal era that followed."
"Virginia has worked hard to move beyond the very things for which Gov. McDonnell seems nostalgic," said a statement issued by the Virginia Legislative Black Caucus.
Virginia was home to more of the war's battles than any other state, and its Capitol in Richmond doubled as the Confederate seat of government.
McDonnell said slavery was not the lone issue contested in the war that ended with Gen. Robert E. Lee's surrender in 1865 at Appomattox Court House, about 75 miles west of Richmond.
"There were any number of aspects to that conflict between the states. Obviously it involved slavery, it involved other issues, but I focused on the ones that I thought were most significant for Virginia," McDonnell said.
Former Gov. L. Douglas Wilder, who in 1989 became the nation's first elected black governor, said no discussion of the Old South or the Confederacy is balanced without mentioning the human bondage it tolerated.
