Product Red, which launched in January, has so far attracted the support of brands such as American Express, Gap, Converse and Giorgio Armani, in its pledge to help women and children blighted by Aids in some of Africa's poorest countries.
The Independent will donate half of the revenue from the one-off May 16 edition to Product Red, with Bono taking charge of the newspaper's editorial decisions.
Bono is expected to devote the paper's coverage to the issues that the various charities and organisations he is involved with campaign for. They include Make Poverty History, Live8 and Data (Debt Aid Trade Africa), which was set up by Red's co-founder, philanthropist Bobby Shriver.
Bono said: "People see a world out of whack. They see the greatest health crisis in 600 years and they want to do the right thing, but they're not sure what that is. Red is about doing what you enjoy and doing good at the same time."
Simon Kelner, editor-in-chief at The Independent, said: "There is a great deal of compatibility between ourselves and Red.
"Bono has a unique insight into world affairs, and, as guest editor, will produce a newspaper that, in the best traditions of The Independent, will be challenging, ground-breaking and exciting."
Bono is has already started work on the paper and is currently commissioning articles for its arts, sports, fashion, politics and health sections, as well as planning special features on Africa.
Bono says Product Red is an attempt to create a "win-win situation for consumers, the corporate sector and the world's poor", by ensuring a percentage of profits from the companies involved are used to alleviate the Aids epidemic in Africa, which afflicts more than 25m people.
The companies currently involved with Product Red have created specially designed products, which will have a designated percentage of profits allotted for Aids relief programmes in Africa.
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