The "Beasts of the Southern Wild" cast member wore a blue dress and carried a puppy purse at the Los Angeles ceremony Sunday night.
Although she lost the Best Actress prize to "Silver Linings Playbook" star Jennifer Lawrence, Quvenzhane still went down in the history books as the youngest person ever to be nominated for the award.
"Everyone else seems afraid to say it, but that Quvenzhane Wallis is kind of a [expletive], right?" The Onion tweeted Sunday night, then quickly deleted the post.
CNET said it was unclear what prompted the mean-spirited barb toward the child on her big night, but attributed its fast removal from the Internet to Onion staffers realizing it was a mistake.
Actor Wendell Pierce was one of the Twitter users outraged by the quip. He demanded that whoever wrote the comment take responsibility and apologize for it.
"Let him defend that abhorrent verbal attack of a child," he tweeted. "You call it humor I call it horrendous."
Steve Hannah, The Onion's chief executive officer, acknowledged Monday in a statement to Fox News the comment about Quvenzhane was "crude and offensive -- not to mention inconsistent with The Onion's commitment to parody and satire, however biting."
"In addition, we are taking immediate steps to discipline those individuals responsible," Hannah wrote. "Miss Wallis, you are young and talented and deserve better. All of us at The Onion are deeply sorry."
Quvenzhane was announced as the star of the new movie musical version of "Annie" Sunday.
2014: The Year in Music [PHOTOS]