The much-awaited amendment by General Pervez Musharraf would free 1,300 women facing various charges until their trial.
Announcing it on Friday, Sumaira Malik, the minister for women's affairs said: "President Musharraf has taken a bold decision to protect the rights of women and save them from the misuse of Islamic laws."
The president has sought to reform Islamic laws on blasphemy and women's rights in the past but backed off because of strong opposition in deeply conservative Pakistan.
Friday's amendment is the president's first to the Hadood Ordinance, legislation based on the Koran and Islamic tradition.
Under the ordinance, women can be sentenced to death by stoning if found guilty of having sex outside of marriage.
Drinking is punishable with 80 lashes, theft with the amputation of the right hand.
However, such punishments have not been carried out in Pakistan as courts from the Islamic and ordinary legal systems overturn each others' decisions in unresolved jurisdictional battles.
Malik did not distribute copies of the amendment, which she described as "a great step by the government", and only said Musharraf had signed it.
Human rights groups say the Hadood Ordinance makes rape prosecutions almost impossible because under the laws, the victim must produce four male Muslim witnesses in court to prove the charge.