Lewis and the Muscular Dystrophy Association recently ended their working relationship after holding fundraising telethons together for more than 40 years.
Jamie Masada, owner of the Laugh Factory comedy club, joined several comedians in protesting Lewis's exit from MDA last month and has now organised an all-star tribute to the comedian.
Fans will able to watch the webathon online and donate money to fight muscular dystrophy.
Masada said that he planned for the webathons to be an annual event until a cure for the disease is found, reports The AP.
Nigel Lythgoe and Alison Sweeney replaced Lewis as hosts of the 2011 MDA Telethon, which raised more than $61m on Sunday.
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Watch a clip from Jerry Lewis's final MDA telethon in 2010 below: