The campaign, created by BBDO NY and directed by Craig Gillespie, will promote Pepsi Stuff, a new marketing effort that features the soft drink maker giving away music and other items in return for customers collecting points.
Timberlake follows in the footsteps of ex-girlfriend Britney Spears, who appeared in advertising campaigns for Pepsi in the earlier part of the decade. More recently, Pepsi has paid stars like Kanye West, Mariah Carey, Mary J Blige, Gwen Stefani and P Diddy to promote it.
Timberlake's ad is called "magnetic attraction", and will have him involved in a number of stunts, narrowly escaping disaster. The idea is to show how Pepsi Stuff "brings people closer to music, merchandise, apparel and more", the company said.
People can already sign up for the Pepsi Stuff promotion, which begins on February 1. Pepsi is describing it as its "biggest promotion ever".
The Super Bowl is always a major event for big-spending advertisers such as Budweiser and Pepsi. However, with this year's Oscars ceremony in doubt because of the US screenwriters' strike, it will take on a bigger significance.
Timberlake was at the centre of the notorious Nipplegate scandal with Janet Jackson during the 2004 Super Bowl half-time entertainment, when he tore off a piece of Jackson's costume to reveal her nipple to the unsuspecting US public and surprised executives at CBS, which was broadcasting the game. Timberlake later described it as a "wardrobe malfunction".