The commercial featured Tennant using Virgin’s TiVo service to catch up on old episodes of the BBC One show and was part of a multi-million pound campaign which launched last month in which Tennant is seen searching for his past episodes using the TiVo personal video recorder and catch-up service.
However BBC Worldwide complained that the advert appeared to be a commercial endorsement of the service, breaking the corporation’s guidelines.
Virgin Media said it had agreed to pull the ad as “a gesture of goodwill”.
In a joint statement, the BBC and Virgin Media said: “Virgin Media has listened to concerns raised by BBC Worldwide about perceived commercial endorsement by the BBC/a BBC brand relating to the recent Virgin Media advertisement.
“As a gesture of goodwill Virgin Media has agreed to withdraw transmission of the advertisement.”