The People's Daily had run the US satirical site's gushing quotes about the "Pyongyang-bred heartthrob" in both Chinese and English as world news, along with a 55-image gallery opening with Kim astride a horse and gazing into the distance.
But after gleeful Internet users pointed out the error, the English version's web address returned a "page not found" message late Wednesday morning.
A link to the story remained on the website's Korean news pages but there was no content.
The printed edition of the People's Daily did not carry the online report, which made no mention of satire.
It quoted The Onion as saying: "With his devastatingly handsome, round face, his boyish charm, and his strong, sturdy frame, this Pyongyang-bred heartthrob is every woman's dream come true.
"Blessed with an air of power that masks an unmistakable cute, cuddly side, Kim made this newspaper's editorial board swoon with his impeccable fashion sense, chic short hairstyle, and, of course, that famous smile."
The People's Daily article was in line with a series of reports carried by state media backing Beijing and its allies.
During the Communist Party's 18th congress this month, Xinhua news agency published a steady stream of stories quoting "world leaders" as praising the meeting.
Many congratulations were from politicians in countries such as Samoa, Guyana, Congo or Montenegro. Obscure groups such as the "Fund of Peace of Republic of Kazakhstan" were also quoted as following Xi Jinping's elevation to party general secretary.
The People's Daily also ran a series of articles citing foreigners lauding the party's showcase event, including one headlined "Reporters highly praise Press Center of the 18th National Congress".
The newspaper's website has previously published other picture slide-shows on Kim, usually depicting the North Korean leader in a heroic pose, on horses or with army generals.
China is North Korea's sole major ally and provides the bulk of its food and fuel imports.
The People's Daily could not be reached for comment on Wednesday.