There are no problems with ads on other pages on Dailymail.co.uk, but the banner, skyscaper and rich media placements on the article by Jan Moir are now blank.
James Bromley, MailOnline MD, said the decision to remove the ads was taken by Mail Online "within minutes" following the reaction to the article.
"This is done frequently and by other newspapers. For example, we wouldn't want a mobile phone ad next to an article about mobile phone masts."
The piece by Jan Moir, a columnist for the Mail, has prompted a storm of comments both on the piece on the Mail's website and in the wider online sphere.
One particular line in the piece, which describes Gately's death as "sleazy", has angered many readers and the wider public. Moir wrote: "Another real sadness about Gately's death is that it strikes another blow to the happy-ever-after myth of civil partnerships."
A Facebook group has been set up calling on people to pressure the Mail to remove the article by contacting advertisers that have appeared next to it and by complaining to the Press Complaints Commission.
Marks & Spencer, BT and Procter & Gamble are among the nine advertisers listed on the group's page, with phone numbers and other contact details.
The group is called 'The Daily Mail should retract Jan Moir's hateful, homophobic article'.
Twitter is also humming with comments about the incident, pushing 'Jan Moir' to the top of the trending topics.
Jan Moir has since issued a statement in defence of her piece, in which she claimed it was "mischievious in the extreme to suggest that my article has homophobic and bigoted undertones" and described the internet campaign as "heavily orchestrated".
She said: "When I wrote that ‘he would want to set an example to any impressionable young men who may want to emulate what they might see as his glamorous routine', I was referring to the drugs and the casual invitation extended to a stranger. Not to the fact of his homosexuality.
"In writing that ‘it strikes another blow to the happy-ever-after myth of civil partnerships' I was suggesting that civil partnerships - the introduction of which I am on the record in supporting - have proved just to be as problematic as marriages."
Moir said it was never her intention to upset people with her comments, and that the point of the piece, "which, I wonder how many of the people complaining have fully read", was that "his death raises many unanswered questions".