MDA executive R Rodney Howell said that Lewis's dedication to helping muscular dystrophy sufferers will never be forgotten, but confirmed that the comic "will not be appearing on [this year's] Telethon".
Lewis had previously announced in May that he planned to retire following the 2011 telecast.
The comedian began working with MDA in the 1950s and went on to front the organisation's Labour Day weekend appeals.
Lewis's annual telethons have raised more than $2 billion for MDA since the first one aired in 1966.
MDA has not yet revealed who will host this year's telethon, which will air for six hours on September 4.
Lewis recently criticised American Idol by referring to the show's contestants as "McDonald's wipeouts".
Watch Jerry Lewis reunite with comedy partner Dean Martin on the 1977 MDA telethon below: