It would be more accurate to call it a draw. It was the fact that they were in enemy territory that made Gen. Lee decide to cross the Potomac back into Virginia. But the actual battle was not a Union victory by any stretch of imagination.
It was a bit like the Battle of the Coral Sea. A strategic victory for the North and a tactical victory for the South.
#5
Battle of Antietam
Date: September 17, 1862
Location: Maryland
Confederate Commander: Robert E. Lee
Union Commander: George B. McClellan
Confederate Forces Engaged: 51,844
Union Forces Engaged: 75,316
Winner: Inconclusive (Strategic Union Victory)
Casualties: 26,134 (12,410 Union and 13,724 Confederate)
Note: "Casualties" = Total Casualties: killed, wounded, missing, captured
(http://www.civilwarhome.com/Battles.htm)