Boyle, known for his controversial material, jested on Twitter that he worried the Olympic athlete would have an advantage at the Games due to her "possessing a dolphin's face".
In response, Walliams said that he was disappointed in the Mock the Week star for targeting someone he considered to be "an absolute inspiration".
"I have met and spoken on the 'phone to double Olympic Gold Medal swimmer Rebecca Adlington. And she is a beautiful woman, inside and out," he wrote.
"It is disappointing that anyone would want to be mean about her appearance. Rebecca's an absolute inspiration, and a really lovely lady."
Walliams continued to voice his support of Adlington as she became the first British swimmer to win medals at consecutive Olympic Games during the 400m freestyle yesterday (July 29).
He wrote: "Come on Rebecca...Bronze! Cool. We love you Becky. Roll on the 800m."
Boyle, meanwhile, has continued to express disbelief in the controversy sparked by what he saw as a relatively tame joke.
Photo gallery - London 2012 in pictures:
"I have an apology for the people of Britain. Sadly it's written on the end of my c**k in a braille you can only read with your tonsils."
Boyle previously attracted 75 complaints from Mock the Week viewers and criticism from the BBC Trust after likening Adlington to "someone looking at themselves in the back of a spoon" on a 2008 episode of the show.
Adlington will compete to win a second medal at London 2012 in the 800m freestyle on Friday (August 3).
Watch celebrities chat London 2012 with Digital Spy below: