The minute-long film, which stars the U2 singer alongside George Clooney, Colin Farrell and Kristin Davis, is part of the Hungry No More campaign which calls for governments to help tackle the causes of famine in Africa.
However, Clearcast, the organisation which approves adverts, claimed that it breached the 2003 Communications Act because of its political content.
A Clearcast spokeswoman told the BBC: "These rules ensure that adverts aren't being broadcast by bodies whose objects are wholly or mainly political. One appears to be caught by this rule as they state that part of their raison d'être is to pressure political leaders.
"It also appears that a number of the claims made in the version of the ad that we have seen are directed towards a political end, which is again against the rules."
However, One's Europe director Adrian Lovett insisted that the foundation is not a political party, nor does it have any political affiliation.
"We recognise the purpose of the broadcasting code is to keep political propaganda off British television," he said. "But our ad highlights the desperate plight of 750,000 people in East Africa who, the UN warns, could die before the end of the year.
"Unless we keep the spotlight on this crisis and the need for urgent action, those people will be forgotten. Who can object to that message? We are challenging this decision and hope the broadcasters will reconsider."
A broadcaster carrying an advert which breaks political advertising rules faces a possible Ofcom fine or a revocation of its licence.
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Watch the banned advert below: