In Act 3, Elizabeth's lie further incriminates her husband and causes the court to distrust Proctor's veracity.
Accordingly, when Elizabeth is brought before Danforth, she refuses to confess that her husband has committed the crime of lechery. All she will admit to is that she was jealous of Abigail, and she imagined that Proctor had become infatuated with the girl. Ostensibly, her suspicions were the only reason she had Abigail removed from the household. Elizabeth states that her husband is a "goodly man" who never turned from her; essentially, she lies to save Proctor. However, Elizabeth makes the situation worse for her husband.
Hale understands how a wife might lie to save a beloved husband, but Danforth seems impervious to such an eventuality. The gullible Danforth is further manipulated by Mary, who now claims that Proctor will murder her if Elizabeth hangs. In the end, Danforth dispatches orders for Proctor to be jailed, and Hale quits the court. Until now, Hale has been arguing for the possibility of Proctor's innocence. After Elizabeth's lie (and Mary's accusation) however, Hale loses his own credibility and is humiliated by his previous, vocal support for Proctor.
Additionally, with Proctor in prison, Elizabeth is bereft of her husband's emotional support during her pregnancy. So, Elizabeth's lie leads to negative consequences for both Proctor and her. In the end, Proctor is hanged for his supposed guilt even though he is innocent. If Elizabeth had not lied, the guilty parties might have been called to account for their own falsehoods.