In the article, reporter Nico Hines -- a straight, married man -- recounted using dating apps like Tinder and the gay-oriented Grindr to meet athletes in the Olympic Village in Rio.
Headlined "The Other Olympic Sport In Rio: Swiping," the article drew angry accusations that Hines had outed gay athletes, whom he didn't identify by name, with his descriptions of them.
Slate slammed the piece as "disgusting and irresponsible," while author and gay rights activist Dan Savage called for the Olympics to revoke the reporter's press credentials.
"So... straight 'journalist' for @thedailybeast probably gonna get some gay guy killed with this piece," Savage tweeted on Thursday.
The Daily Beast initially responded to the criticism by making some changes to the article and publishing an editor's note. But it later admitted that didn't go far enough.
"We initially thought swift removal of any identifying characteristics and better clarification of our intent was the adequate way to address this," read a subsequent editor's note explaining the article's deletion. "Our initial reaction was that the entire removal of the piece was not necessary. We were wrong. We're sorry."
The Daily Beast said the article didn't live up to its values, such as "standing up to bullies and bigots, and specifically being a proudly, steadfastly supportive voice for LGBT people all over the world."
"This was a failure on The Daily Beast as a whole, not a single individual," the editor's note added. "The article was not intended to do harm or degrade members of the LGBT community, but intent doesn't matter, impact does."
Hines, whose Twitter account was bombarded with furious messages, declined to comment by email.