Krigstein's "Master Race"
Note: to avoid spoiling the ending, don't click through to any of the links discussing the story until reading it yourself.
Bernie Krigstein's "Master Race,"* which appeared in EC Comics' Impact #1, is deservedly one of the most famous and acclaimed comic stories. Not only is the art top-notch and the techniques striking, but it's quite remarkable that this shocking story was published just ten years after the end of World War II, before the Holocaust had been widely depicted in popular media, much less in comic books. My copy of a reprint of this is in storage right now, but some helpful soul made high-quality scans of the 8-page story and posted them on their Geocities page (click on the scan to go to each next page).
Read (or re-read) the story first and then check out these essays on it and Krigstein by Martin Jukovsky, Paul Gravett, and Art Spiegelman.
*Krigstein illustrated the story and is most associated with it, but Al Feldstein wrote it.