The all-star Love for Levon benefit concert for the family of the late drummer also featured music and anecdotes from My Morning Jacket, Warren Haynes, Joe Walsh, Ray La Montagne, John Prine, Lucinda Williams and John Mayer.
The Izod Center get together was staged in a bid to raise funds to help Helm's family retain ownership of his home and converted barn-studio in Woodstock, New York, where the rocker hosted his celebrity-packed campfire-style sessions called Midnight Rambles.
Waters' unannounced appearance was a highlight of the Love for Levon concert and he wore a battered red cap Helm gave him after they performed together in Berlin, Germany two decades ago.
The former Pink Floyd star vowed to keep it close "until the day I die".
Waters then performed Helm's Wide River to Cross with the late star's daughter Amy.