The satirical newspaper on Sunday referred to Quvenzhane Wallis with an expletive intended to denigrate women. The Onion was lambasted overnight and asked for forgiveness Monday.
"It was crude and offensive — not to mention inconsistent with The Onion's commitment to parody and satire, however biting," The Onion CEO Steve Hannah wrote on Facebook. "No person should be subjected to such a senseless, humorless comment masquerading as satire."
Hannah said the offensive tweet was taken down within an hour and the newspaper has "instituted new and tighter Twitter procedures" to ensure it will never happen again. Those responsible would be disciplined, he added.
"Miss Wallis, you are young and talented and deserve better. All of us at The Onion are deeply sorry."
A message sent to Quvenzhane's representative seeking comment wasn't immediately returned Monday. She was the youngest-ever actress nominee at the Academy Awards.
The Onion's original tweet brought some calls for the fake news organization to publicly identify the writer of the tweet, vows to refuse to retweet its material, and requests from outraged consumers to email The Onion to complain.
Oscar host Seth MacFarlane also joked about the young star during the ceremony. Some found the quip offensive, albeit not to the degree of the outrage over The Onion's tweet. MacFarlane joked that "it'll be 16 years before she's too old for" George Clooney.
Despite the attack, Quvenzhane had some reason to stay positive Sunday. By the time she'd arrived at the Oscar telecast, she could boast that she had been cast to play Annie in a contemporized adaptation of the Broadway musical and the "Little Orphan Annie" comic strip to be directed by Will Gluck.
It wasn't the first time The Onion has gotten into hot water for trying to push its humor. Last year, the site attracted public ire for an image that showed an airliner about to crash into Chicago's Willis Tower. Despite an outcry, the Onion's marketing director refused to back down.
Last year, the joke site made international headlines when the online version of China's Communist Party newspaper hailed an Onion report naming North Korean dictator Kim Jong Un as the "Sexiest Man Alive" — apparently unaware it was satire.
In 2011, U.S. Capitol Police released a statement refuting tweets and an article claiming members of Congress had taken a group of schoolchildren hostage. It included a doctored picture of Republican House of Representatives Speaker John Boehner holding a gun to a child's head.
The Chicago-based publication was founded in 1988 by two students in Madison from the University of Wisconsin. Starting as a local college newspaper, it became a national comedy institution and went online in 1996, and has since developed a television news parody.
The publication is distributed weekly in cities, but it has also embraced Twitter and has an app for the iPad and other tablets. It says it averages 40 million page views and roughly 7.5 million unique visitors per month.