The New York-based news and gossip site removed a story about a reportedly gay sexual solicitation by a married man who is the brother of a former Obama administration official.
Some critics said the post was a type of blackmail and the removal was condemned in the media. At least one advertiser put ads on hold in protests.
In statements made on Monday 20 July, the two senior staff who resigned - executive editor Tommy Craggs and Gawker.com editor-in-chief Max Read said the removal was a betrayal of the site's pledge to editorial independence.
Craggs said he "would have to resign if they voted to remove a story I'd edited and approved.
"In the wake of Friday's decision and Tommy's resignation I can no longer sustain that belief. I find myself forced to resign, effective immediately," Max Read, the editor-in-chief of Gawker said in his email to the managing partners.
Nick Denton, the founder and chief executive of Gawker Media, said in a blog post that the company's flagship site was wrong to publish the story.
"The media environment has changed, our readers have changed, and I have changed," Denton wrote. "Not only is criticism of yesterday's piece from readers intense, but much of what they've said has resonated.
Some of our own writers, proud to work at one of the only independent media companies, are equally appalled."
Denton said the story's deletion was the first time the site has "removed a significant news story for any reason other than factual error or legal settlement."
The company's managing partnership voted 4-2 to remove the post. (Originally the vote was reported to be 5-1), according to CNN Money.
The dissenting votes came from Heather Dietrick, Gawker's chief legal counsel, and Tommy Craggs, the executive editor.
Soon after the vote, the editorial staff issued a statement condemning the vote. "Our opinions on the post are not unanimous but we are united in objecting to editorial decisions being made by a majority of non-editorial managers. Disagreements about editorial judgment are matters to be resolved by editorial employees. We condemn the takedown in the strongest possible terms," the statement said.
However, Denton took full responsibility for the removal of the post, according to a Guardian report.
"This was a decision I made as founder and publisher... I was ashamed to have my name and Gawker's associated with a story on the private life of a closeted gay man who some felt had done nothing to warrant the attention."