The cartoon published Friday in an early edition of Munich daily Sueddeutsche Zeitung prompted complaints of anti-Semitism from Jewish groups.
Later editions showed an empty hole where Zuckerberg's face had been.
Cartoonist Burkhard Mohr says he had intended to make a point about Facebook devouring rival WhatsApp and didn't realize the caricature resembled the kind of incitement to anti-Semitism printed by the Nazis.
Mohr told The Associated Press that he deeply regrets "this misunderstanding and any readers' feelings I may have hurt."
Facebook didn't immediately respond to requests for comment.