News of the partnership has been timed to coincide with the World Economic Forum in Davos.
As part of the deal, the US soft drinks giant will invest management expertise and £4.1m in cash into two long-term water projects.
The Earth Institute will receive the lion's share of the funding, while Damon's H20 Africa charity will receive $2.5m from PepsiCo's corporate budget.
It is hoped the involvement of Hollywood star Damon will help spread the message about the urgency of clean supplies to the estimated 1.1bn people currently without access to safe drinking water.
Damon, who won a screenwriting Oscar in 1998 for 'Good Will Hunting' and is known for playing trained assassin Jason Bourne, set up the charity to provide wells on farms and sanitation in countries from Mali to Uganda.
He said in the Financial Times: "Pepsi is dwarfing all our efforts in the last two years [but] it's not just a cheque. I'm hoping this is a beacon everyone else succumbs to by irresistible example."