Users logging into the App Store will now see the top 25 apps highlighted in red, including 'Angry Birds', 'Despicable Me: Minion Rush', 'FarmVille 2: Country Escape' and 'Frozen Free Fall'.
Over the next two weeks, Apple will donate all proceeds from downloads of these apps or any in-app purchases.
The initiative will run until 7 December, and the apps also feature exclusive new content to boost downloads, such as extra game levels.
Apple will also donate a portion of sales made during Cyber Monday (1 December) to the Global Fund to fight Aids.
Cyber Monday is the first Monday after Thanksgiving in the US and is usually considered one of the biggest online shopping days of the year.
On Black Friday, which marks the beginning of the shopping season, Apple will hand a (Red) iTunes gift card to any US customer making a purchase, and donate a percentage to the Global Fund.
Apple hasn't said how much it plans to donate with each purchase to the Global Fund, however (Red) co-founder Bono said the company had donated $75m to date.
Though Apple is not feted for its corporate philanthropy, this is not the first time the company has been involved with (Red).
Last year design chief Jony Ive, designed a bespoke camera for the charity's auction at Sotheby's, which went on to sell for over $1m. The company has been participating in (Red) since 2006.
This is the first time Apple has extended its support for (Red) to the App Store.
Tim Cook, Apple's chief executive officer, said: "Apple is a proud supporter of (Red) because we believe the gift of life is the most important gift anyone can give.
"This year we are launching our biggest fundraising push yet with the participation of Apple’s retail and online stores, and some of the brightest minds in the App Store are lending their talents to the effort as well."