The ad, 'Unacceptable', was due to be launched with an event at Wembley Stadium tomorrow (11 February). Leading figures from the football world and prominent members of the lesbian, gay, bisexual and transgender community were scheduled to speak at it.
The FA blamed the decision on postponing the event on needing more time to work on a long-term strategy. Gay rights campaigners have criticised the move.
According to an Ogilvy spokesman, the FA and Kick It Out approved seeding of the film after learning yesterday that it was to be shown on Newsnight last night.
The spokesman did not know how Newsnight obtained a copy of the film, but said when the FA and Kick It Out learned that it was planning to show the copy it had, they asked the agency to send the final version to the programme.
However, an FA spokesman said the FA was not yet pushing the ad out itself, because it was waiting for the green light from its stakeholders to do so.
A Kick It Out spokesman said the group was happy that the ad was online but it would not put the ad on its own YouTube page until it got sign-off from the FA. The spokesman said the sign-off was "hopefully" coming either tonight or tomorrow.