Preparing for a tour that includes Australia, the Mexican-American rocker told Australian Associated Press: "Beyonce is very beautiful to look at [but] it's more like a modeling kind of music - music to model a dress. She's not a singer singer, with all respect to her."
As for Adele, "she doesn't bring all the dancers and props. She can just stand there and [sing], and that's it. This is why she wins."
He was referring to Adele's performance at Sunday's Grammys, where the British star simply sang, while Beyonce put on an elaborate show with dancers and a matriarchal theme.
Santana now says he meant to praise Adele, 28, but not to denigrate Beyonce, 35, who "deserves all the accolades that come her way."
Beyonce has won 22 Grammys but never album of the year. Some fans think it's due to racial bias.
Santana, 69, won album of the year with his band in 2000 for Supernatural.