In Act 3, scene 3, John confesses to the courts that he has had an affair with Abigail. He does this in order to stop the court hearings and save his wife's life, who has been accused by Abigail. When Judge Hawthorne brings in Elizabeth to corroborate John's confession, Elizabeth is torn between telling the truth and saving her husband's reputation. Against her better judgment, Elizabeth lies to the court because she thinks she is saving her husband. However, her lie only makes Abigail’s accusations stronger in the courts eyes. This is ultimately what leads to the death of her husband.
This is an important question in understanding the evolution of the relationship between John and Elizabeth. The three key players all know what's at stake (Danforth, John and Abigail), however, Elizabeth only knows that her moral ethic is torn. On the one hand, if she lies to save her husband's reputation, she may go to Hell, on the other, if she tells the truth, her family and her husband's good name is destroyed. It is not simply that she says, "(faintly) No, sir." to save John's reputation, but that she is willing to condemn herself with the lie. This moment is not only the pivotal point in the play that determines Abigail's innocence in Danforth's eyes, it is also the resurrection of the intimacy between John and Elizabeth. Both now know each other's love and willingness to sacrifice for their love.