Atticus asks Mr. Ewell to write his name on the back of an envelope, which establishes that he is left-handed. Atticus then questions Mayella and hears from her what she has already testified to, that Tom Robinson jumped her from behind, choked, beat her on the right side of her face, and raped her.
After this, Atticus has Tom Robinson stand, which reveals that his left arm, which would have left the bruises on the right side of her face, is withered and twelve inches shorter than his right arm due to an accident in a cotton gin when he was young.
At this point, Atticus asks Mayella "how" Tom could have raped her. He follows up by asking how he could have punched her repeatedly on the right side of her face with his crippled arm, why none of her siblings heard her screaming, and how she couldn't manage to fight the handicapped Robinson off. He ends by asking her if her father was really the one who assaulted her.
Despite Mayella's denials that it was her father and insistence it was Robinson, Atticus has established a more plausible alternative as to her attacker. Mr. Ewell is left-handed, which is consistent with her having been punched her on the right side of her face, which Robinson could not have done.
After the trial, Atticus explains to Jem that ingrained racism takes over even for reasonable white men who serve on a jury in the South:
In our courts, when it's a white man's word against a black man's, the white man always wins. They're ugly, but those are the facts of life.
He adds that when a white man convicts a Black man he knows is innocent, that man is "white trash."