The Tory clearly surprised fellow guests on BBC One's Andrew Marr Show when she made the remarks following an impression of Mr Farage by comedian Rory Bremner.
Mr Farage later said he was "astonished" by the "foul-mouthed attack" and insisted the minister had "stooped to the levels of crudity that any politician would spend a lifetime apologising for".
During a light-hearted discussion at the end of the show, a chuckling Ms Soubry made a gesture with her finger and said: "I always think he looks like somebody has put their finger up his bottom and he really rather likes it."
Mr Bremner said: "Are you allowed to say that?"
In a statement, Mr Farage said: "This latest, remarkable foul-mouthed attack is utterly incredulous."
Ms Soubry said: "It was a light-hearted remark."